HAving gone through every tick box one by one with a sequence of numerous options, I narrowed down the problem to be the Minfy check box.
I was having server 500 errors, .htaccess corruptions, this that & ever other issue, until going through the various/numerous options one by one over a good 9 hour period & testing each option via I.E | chrome & http://gtmetrix.com/ - it apparently caused the majority of the issues.
So, I've had to uncheck the option and use another programmers tool to have that part of WP working efficiently.