Usually ""hacked" roms" have oem's built into the rom. Who's rom are you running? or if you made the rom yourself tell us which kitchen you used. And/or what other oems you might have added to the kitchen.
also you could try looking in the thread the rom makes posted the rom in for similar problems.

If you're not using a task manager, it could be that you just have a lot of un-exited apps running in the background. The "X" button by default only hides an application in windows mobile.

If hard-reseting is your only fix I don't think that's the problem though as a regular soft-reset should fix that. Sounds more like you have very low storage space, maybe due to a large inbox, temp files, PIE cache, ringtones, pictures, anything like that.

list the progs running...
list the rom using...
list what you have done exactly (backups, cleanups)

EDIT:
not all backups & cleanups are safe.,, example:
Member Bushrod in WM6 bug thread :
"If you use Memmaid 2.0, do NOT try Jump To>Tweaks>System Tweaks and click Apply. I did that and lost my SD card. After further testing, even going there and hitting "Apply" without changing anything made me lose my SD card. I could only get it back with a hard reset."

Sory but untill all your steps are realized this is a guessing game .

I am currently running WM6 with the HTC Home and TodayAgenda plugins with complete stability and performance so far.