that sounds bad. Safe Mode is supposed to be only NECESSARY software, as in that which is crucial for it to work. Try to run Malwarebytes again in a few days, as well as any other software.
also, consider using a recovery disc and doing a fixmbr and fixboot command, in case its hidding in your bootsector.
Personally, if the infection is bad enough to damage Safe Mode I would Re-format the computer, after backing up all files/folders i care about and erasing the drive. Drastic, but effective.
also, MyNetWatchman makes SecCheck [http://www.mynetwatchman.com/tools/sc/] that will scan for any open network connections/running programs, and compare them to a vast database. anything flagged red or unknown is an area of interest.





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