Having SafeCopy enabled/disabled will make absolutely no difference to the scan time (it's only used when 'writing'). It's actually not 100% clear if your timings as quoted are for the whole run or just the scan stage. Naturally, the whole run will depend on what work there is to do (stuff to copy, etc), which may of course vary between runs.
As stated, I believe V6 uses some different Windows API calls to V3, and these may not be performing optimally on your PC (note: you still haven't stated which one(s) are running which version(s), so knowing which is 'Source*' doesn't tell us how it is being scanned). But if there are no error messages, we wouldn't be able to see any reason for that, even with debug output - all we would see is that it took X seconds (or whatever) for a particular operation, with no 'explanation' sent back by Windows. Basically it either carries on till it finishes, or it stops (with an error message). There's no 'in-between' state.
EDIT: I'm still confused why you mention 'Source' for a Synchronize profile that you created from scratch in V6, because such a profile should show Left & Right...
As stated, I believe V6 uses some different Windows API calls to V3, and these may not be performing optimally on your PC (note: you still haven't stated which one(s) are running which version(s), so knowing which is 'Source*' doesn't tell us how it is being scanned). But if there are no error messages, we wouldn't be able to see any reason for that, even with debug output - all we would see is that it took X seconds (or whatever) for a particular operation, with no 'explanation' sent back by Windows. Basically it either carries on till it finishes, or it stops (with an error message). There's no 'in-between' state.
EDIT: I'm still confused why you mention 'Source' for a Synchronize profile that you created from scratch in V6, because such a profile should show Left & Right...