Partition Merge Error (35000)

Hi, I originally created a design using an earlier Quartus version (11.1 SP1) which I am now trying to compile using Quartus 13.0 SP1 (the newest version I can use for Cyclone II devices). While the design had compiled fine with the older version, now I keep getting the following error:

Error (35000): Port "mod_clk~1" does not exist in the interface of the partition "Top", but another partition attempted to connect to it

Since this is a small design and I am using the WebEdition, I don't know what that "another partition" is all about - as far as I am concerned, I don't need any partitions at all.

I found the thread http://www.alteraforum.com/forum/showthread.php?t=40775 which suggests it might be a SignalTap II problem. So I disabled my SignalTap II instance, but the error still persists.

Any suggestions what I should try next?

update:

Using the RTL Viewer, I found that "mod_clk~1" is an internal node generated by Quartus' synthesis and I don't have any (manual) references to it in the QSF file. I also found that Quartus always automatically adds the following line to the QSF file, even after I manually delete it:

set_instance_assignment -name PARTITION_HIERARCHY root_partition -to | -section_id Top

I tried compiling a different top-level entity, which worked successfully, so this line doesn't appear to be the problem.

update 2:

I tried deleting the db and incremental_db directories as well as all files except the QPF and QSF from the project folder to see if this problem is caused by some outdated information. It doesn't make a difference, after the Analysis & Elaboration step, the Partition Merge step fails with error 35000.

update 3:

Just to make sure that I didn't corrupt anything, I installed Quartus II WebEdition 11.0 SP1. I opened the same project and simply compiled it - without any errors. So it seems to be a problem with the Quartus 13.0 SP1 version...