Could you try re-downloading the Cytoscape installer? This sounds like it could be a corrupt installer. Also, if you are on a 64-bit machine, be sure to download the 64-bit version of the installer - judging by the error you got, it seems like you may have been using the 32-bit installer on a 64-bit machine.
If that doesn't help, there are a few other things that you may want to check:
1) Does your user account have administrative permissions? If not, you may want to try installing with an administrative account (if possible) or installing to your user directory rather than Program Files.
2) Does your hard disk have plenty of free space? If it is low on space, you may want to try freeing some...
Hope this helps...
Tim