I've had an issue with slow execution of builds for a while on cygwin.
I was forced to update yesterday and ran into the issue of rebaseall simply failing to execute. This forced me to dig into other things and I found a report that Trusteer Rapport/End Point Protection has been known to cause issues with rebaseall, and slow response times. So I removed it, via the normal Windows Uninstall Programs method via Control Panel.
I then did a rebaseall from the dash interface run as admin.
So this means, (win7) from the start menu type dash. The dash shortcut will appear, Right click to run as administrator. Then when it's up, execute :
Go for a coffee... It will sit for a few seconds before it should display output, if it sits and does nothing for more than 5 minutes, you have another issue.
This fixed the rebaseall, but has also massively increased the speed of my build. Worth checking to see if you have it installed, try removing it.