Wouldn't it be nice if things worked as they were supposed to?
So partitions in ISE are going to be removed in version 12.1 and they will then only be available in PlanAhead. This means that Xilinx won't fix any of the many wonderful bugs in their partition implementation.
Two bugs that I've experienced with partitions:
1. Modify a source file that causes ISE's automated uninitiated parsing of source files to fail and all partition information may be removed. That depends on how badly the parsing failed. This sucks as ISE will parse your source files as soon as you set focus back onto ISE, and of course you may not be done editing your source files at that moment. (It should be noted that I use an external editor for my source files.)
2. INTERNAL_ERROR:Xst:cmain.c:3446:22.214.171.124 -
I don't know what this error is but it won't let my partitions work...
I've of course removed all partitions from the design.
hoping you have better experience with partitions