Nothing available from Stardock's software on 'myaccount' will be an issue or 'unsafe'. Some AV programs give false-positives when dealing with some compression algorithms and/or any executable, however the easiest way to not suffer them is to set Stardock's site as 'trusted'.
GUI/Shell software often gets flagged because it is intended to alter the OS and/or system files which is of course what a virus wants to do.
Difference is....one is what you want....the other is what you don't want....and some AV systems can't differentiate...