We had these messages very often too ... no cap no resistor helped. signaltap worked but flashprogrammer failed.
The only solution we had to permanently fix this was to creat a new sopc target design from a clean folder.
I don't know if you have moved from Q4.2 to 5.0 like we did. But here the SOPC target folder was created with Q4.2SP1 and then the design moved to Q5.0. we recompiled the sopc target with q5.0 but nothing fixed this mess.
So try to create a complete new sopc target "mktarget....." with Q5.0 .. here this messages never appeared again.