Hi, I'm one of the developers for IntelliScreenX. Just a reminder for anyone experiencing crashes: They are by far our number one priority to fix. Crash Reporter from Cydia is a pretty good tool for sending them to us. As soon as we receive a crash log (that's something wrong with IntelliScreenX, of course), we can get the fix out the same day 99% of the time.
For example, the alarm popups thing: I'd love it if someone would show me a crash report for that problem. No one should have to "just avoid something" or "live with it" because it crashes.
However, almost all of the crash reports we receive don't have anything to do with IntelliScreenX. The easiest way to tell which tweak is at fault is to look in the crash report and look under backtrace for whichever thread crashed. Usually, it's thread 0 (the main thread), so it will say "Thread 0 Crashed:". Then whichever tweak comes up in the backtrace is usually at fault. Often there are multiple tweaks in there, and generally "whoever touched it last" (i.e., whoever appears nearer to the top of backtrace) is the tweak that has to be fixed to prevent the crash.
Sometimes, the backtrace is unclear because it says "Last Exception Backtrace" in which case a specialty tool is necessary to figure out what caused the crash. Other times, no tweaks appear in the backtrace and those are the hardest to figure out. That means some unknown tweak changed something and somewhere down the line caused Apple's code to crash (instead of right away). However, that last case is rare.