When using XST as the main synthesis tool, incorrect netlists may be used within the PlanAhead environment. After loading all the NGC files representing different Reconfigurable Modules, the first file loaded is the one that will be used in all Configurations.
How do I work around this and when will it be fixed?
The workaround is to simply close and then reopen the PlanAhead project once all the design netlists have been loaded. After this has been done, the netlist references have all be set properly and the project can be used safely.
This has been fixed in PlanAhead 11.3.