Why does my SD data get messed up when i connect to PC with USB?
It sounds like your ROM doesn't properly reset settings when the sdcard is re-enabled (since it obviously becomes unavailable to the OS when using USB Mass Storage). Unfortunately, this is likely an issue with your ROM and I don't think there is a likely setting that would fix it.

However, in Android 3.0, Google added MTP (Media Transfer Protocol) support and it has been in all versions since. This allows the sdcard to remain mounted in the Android system while also allowing it to be accessed on the computer. I can't remember the exact layout of ICS, but to be able to change it to MTP from UMS, it is probably pretty close to Settings -&gt; Storage -&gt; Menu -&gt; USB Computer Connection -&gt; enable MTP