I have to assume you are using GPUs on scrypt givern your numbers.  Regarding GPUs, as has been posted roughly 2 billion times in this thread (albeit mostly for bitcoin), if you change drivers or SDK and then later upgrade cgminer where there are any kernel changes at all, you changed settings.  This is because you made cgminer compile new kernels on a different driver/sdk combo.  Copying a batch file or other breed of launch script doesn't change what you did to your mining machine between cgminer versions.  If you delete the scrypt kernel files from 3.2.1, you will probably see the same slowdown when you run it again and it generates new ones  You'll need to back them up first to test this.  Once it is confirmed, you will need to either revert to the old kernels on the old version, copy the old kernels to the new version if they have the exact same file names, or try to find the magic driver / SDK combo again to get the new version to compile new kernels with the best speed (deleting kernels from the new version between each attempt, probably pulling out lots of hair, and most likely making things worse before you make them better).

ETA:  In your case, you switched to a new folder, so even if there were no kernel changes, you compiled new kernels on new drivers.  I referred to this point in the fix options (copy the old kernels to the new version implies they are in different places, just like copy the batch file to the new version does), but didn't otherwise make it clear in my original response, so wanted to add it.