problems with segmented buffer in SignalTAPII

As long as the clock used by Signaltap is properly defined in timequest it should be correctly analysed. So if you don't get any critical warning it means the timing is fine.

The other explanation I would see is that some bits are skipped or added in the JTAG flow during the transfer. Are you using an external Blaster? Do you even get errors on the JTAG transfers?

We had this problem once in a very specific case, using a non-Altera blaster, on a system running under Linux. There seemed to be a conflict between Signaltap and the Linux FTDI driver which caused problems during the data transfer.