Mod_fcgi causing issues with PHP output buffers

Hi all -
We’re running mod_fcgi, which is working mostly very well, however one of our applications is using output buffering quite heavily - ob_start, ob_clean, ob_flush and ob_end functions, and is causing both Internal Server Errors in many places as well as “strange” behaviour. I can provide some code snippets for those interested, but I wanted to see if anyone has seen this before and/or has any input on this in general.