ISE and ChipScope weird issues

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Hi to all,

These are some issues I noticed about xilinx ise6...I'd like to share with you, and benefit from your feedbacks

I am working on Virtex-II FPGA...implementing mpeg2 decoding system on the V-II 4Milion...I use chipscope as a debugging tool to monitor internal signals and compare them with simulation...

This is working fine, but sometimes I notice some differences in performance between two identical trials; one with chipscope core included and one without...it sometimes leads to one working trial and the other is not...
This happens randomly...meaning that in some trials when including chipscope core it improves performance and in other trials degrades it...

I also notice some changes in system performance when running Xilinx ise par on different machines, using same input files for all and applying same settings...is it affected with differences in computers hardware...!!!

my platform is P4 2.8GHz, 512 DDR...running winXP-SP1
I am using ISE6.2i with chipscope

your comments are very much appreciated...

Thanks,
afnam