EW Publishing Conflicts

When publishing with EW, the timestamps on the server and your computer can be different (sometimes I think the server itself may be part of the problem.  Some have auto backup systems that may be messing with timestamps as I have had this problem as well as others who use this forum).  Unless you have EW3 the SP1 update may not apply to you but this I am not sure of.  To publish just the pages you want in the EW publish area - select the pages you want by ctrl+clicking for multiple pages or just clicking on the page you want.  Then click the arrow button in the center pointing to the right.  This will publish only the pages you have selected.

The software is not the problem.  The problem is the timestamp differences which as far as I know all of them go by.  That way you don't overwrite something on the server unintentionally.  Even 3rd party ftp's use timestamps.  This is so more than 1 person can edit a site.  With 90+pages it is going to take a while for any program to upload.  What I would do is ask your server to turn off the auto back up for your site.  That way the timestamps don't change and see if this resolves the problem.  

In the publishing view it has a changed pages option on the left side, just above the windows where all your files are.  You can change that and then select what pages you want to publish from that.