I know I'm a bit late in menting this, but a few posts back there was a bit of confusion with where 'make clean' should go. I think people may have been getting confused with 'make distclean'. 'make clean' should just remove old object files, etc (things generated AFTER make is executed) leaving the configure file, etc intact. 'make distclean' will do the same as 'make clean' AND it will remove the configuration file, etc too. So 'make clean' should be safe to run after a autogen or configure command, 'make distclean' won't be safe. If you get an error when you type make clean that there is nothing to be done, that usually means that it's already clean.
I would imagine a good thing to do when building a new version is definitely to run 'make distclean' first to clean out old configs as well, especially if the build process has changed. Even better would be to just 'sudo rm -r ' and do another git clone of the repo, then you know you are safe and don't have anything lying around if you are having problems with the build process.
I realise this was not the original posters problem in the end, but just though it should be mentioned for when people compile other things.
Alex
The problem is that with cgminer 3.4.1/2 there is a completely new configuration, so yeah anyone upgrading really needs to ensure they aren't skipping the autogen and configure ... so it's easier to say: rename the old directory (so you can get any config files or scripts from the old directory, if needed after you rebuild) and start again with an empty cgminer folder or fresh git clone ... even I made some mistakes with this back about 2 or 3 months ago when I was doing libusb version testing (and failed to switch the versions properly a few times)
OK, here's where I'm at. I decided to do an upgrade to 13.04 64bit - fresh install of everything. This time I didn't start my p2pool node, opting to straight forward mine on a pool instead for testing purposes. The result is actually worse than with 12.04 I'm afraid, cgminer is now using 37% cpu:
Not sure what to make of this now, but for sure 37% is way too high for 40 usb sticks, and there's absolutely no chance of a previous build corrupting this one - it's all brand new........
I'm now ready to accept any and all possible solutions, no matter how ridiculous or far fetched they might sound - I really don't want to reduce myself to using the "other" mining software from "he who shall not be named"