This sounds like exactly a problem I've been having. A customer had a e-Studio 550 and every so often when the scan logs reached 999 the controller would crash and we would have to re-format / re-install the software on the hard drive. Since then things have gotten worse and the controller won't boot at all now even after re-installing the software.
Good luck with the problem and let us know if you find a solution
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-Tom-