A lot of work has been done to clean up Marlin's code base and especially the Configuration.h files. You can't just drop an old Configuration.h file into the directory and compile. You should bring up Notepad++ and use the Visual Diff add in to to cross all of your settings over to the new format. Also... A bug was found in the stepper motor driver a while ago. It is fixed now. But one of the side effects of fixing the bug is acceleration numbers that used to work OK might be too agressive now. You may need to bump the acceleration down. You might try cutting it in half and see if that makes a difference. If it does, you can start bumping it up until you start having problems.
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