Oh! You don’t need to do anything like that. Just upgrade manually.
You installed via a wbm, so upgrade via the wbm from Webmin.com using the Webmin:Webmin Configuration:Webmin Modules page.
Finally got it working, wahoo 
This is what I did:
From my server I downloaded
/usr/libexec/webmin/virtual-server-theme/left.cgi
Commented out line 80
line 80 is-
@doms = &virtual_server::list_visible_domains();
Renamed the original left.cgi file on the server (effectively backing it up) then uploaded the commented out left.cgi file.
When you load Virtualmin the Webmin part now works in the left menu (rest still broke).
Click
Webmin > +Webmin > Webmin Configuration > Webmin Modules
From http://download.webmin.com/download/virtualmin/ I downloaded virtual-server-3.59.gpl.wbm.gz (http://download.webmin.com/download/virtualmin/virtual-server-3.59.gpl.wbm.gz) and uploaded it to my server (I put it in /downloads/).
From the Webmin Modules page I left the "From local file" ticked and used the browse button (…) across from it to browse my way to the file /downloads/virtual-server-3.59.gpl.wbm.gz
I left all the other settings at their defaults and clicked the Install Module button.
And it worked
This didn’t update the left.cgi file I’d edited, so went back to where that file was and restored the renamed backup (I renamed the commented out left.cgi then renamed the original back to left.cgi, there’s other ways of backing up files, but I find this the easiest way to track changes on my own system).
This fixes the Perl menu error listed in this thread and updates Virtualmin to 3.59. I don’t think it solves the automated update problem since under VirtualMin Packages I still see the option to update wbm-virtual-server is still there, so if the developers don’t do something I suspect I still won’t be able to automatically upgrade to 3.60 when it’s released.
Fixed for now though.
BTW I rebooted the system before reverting the commented out version of left.cgi, (just in case there was a new file and a reboot was needed to activate it: there wasn’t new file) but not sure it’s needed?
And that’s how you explain something like this to people (like myself) who are not comfortable messing around with servers
David Law
Hey David,
Thanks for the update. I obviously wasn’t aware of how dramatic this problem was–I didn’t realize you couldn’t even browse to the Webmin configuration page with the broken theme. 
But, here’s how you can do the manual upgrade without making any file changes:
Browse to /webmin/ on the system (e.g. I would browse to https://www.virtualmin.com:10000/webmin/ ). This will take you out of the framed theme, and remove the left menu from the equation entirely…and allow you to click on "Webmin Modules".
From there you can upgrade to the 3.59 wbm package…which fixes the left-hand menus.
No need to reboot after this change. Just force your browser to reload the whole page. I believe upgrading the module will cause Webmin to restart, which is also needed.
BTW-The above recommendation to install manually using rpm with the --noscripts option is far less dramatic and complicated than modifying the Perl code, isn’t it? I didn’t mean to make it sound super scary, I just wanted to make sure you backed up you configuration before doing the upgrade. You should be making regular backups of everything, regardless.
I suspect the next version of the package will allow overwrites of wbm packages, but, again, doing the bits I documented above will get you onto the RPM version and is not particularly risky…Apologies for making it sound more dangerous than it is.
Update on this.
Got two Virtualmin servers now, one with the poorly thought out setup (see this thread) and the other using the install.sh file which automatically updates whenever there’s an update. Have a slight problem with installing the spam filters in the correctly setup server (another thread) so while I was here thought I’d add some more info here.
I just updated the poorly thought out version from 3.62 to 3.67 manually since in 3.62 the auto update still didn’t work.
Tried to update to 3.67 in one go, but Webmin was out of date, was 3.3 when current Webmin is 3.7 and the 3.67 version of Virtualmin wouldn’t update as a Webmin module with Webmin below 3.4.
Wrongly assumed installing an earlier version of Virtualmin (3.63) would update Webmin, which it didn’t. Kept making that assumption all the way to 3.66 of Virtualmin until I updated Webmin though the Webmin update Vebmin module (or whatever it’s called) which took Webmin to 3.70 adter which I could manually install Virtualmin 3.67 (I’ve had a fun afternoon :)).
Through the various Virtualmin updates I checked the Virtualmin packages update page and didn’t see Virtualmin out of date, which I assume means the free version of Virtualmin hasn’t had the way it updates changed since I had this problem.
So looks like I’ll be manually updating Virtualmin for as long as I have the server in it’s current configuration. Would be nice to not have to go to all this trouble.
Are there any plans to change Vitrualmin to allow automatic updating when we’ve setup a server in this way?
David Law
I honestly couldn’t say, I know the recommended way to install Virtualmin is using the install.sh and the repo’s – I’m not sure if there’s anything in the works to have it check for updates when installed via a module.
You could always pop a question in the bug tracker, Jamie would be the one who’d know
-Eric
I was going on what Joe said:
I suspect the next version of the package will allow overwrites of wbm packages,
I was hoping by now that the free version worked the same way as the paid version: earlier in this thread I think it was Joe that said the paid version allows for automatic updates (some restriction was turned off) with the way many installed Webmin/Virtualmin, but he didn’t know if the free versions restrictions on what it could automatically update from could be turned off to allow automated updates.
Hope that makes sense.
David Law
The Security Updates module supports several methods of updating, including .wbm modules (and tarball Webmin/Usermin). And, it can be setup to update RPMs or debs without using install.sh.
How did you install originally? We need to know specifically, in order to give specific directions (all are a bit complicated, so I’m not going to try to cover them all in a forum post, but I will see about getting some documentation on this in place soon):
Webmin - Tarball, RPM, or deb? Did you use Jamie’s Webmin.com yum or apt-get repository?
Virtualmin modules - .wbm, RPM, or deb?
Do you have the security-updates module installed?