I have a workaround which might help you, if you haven't tried it. I have a weekly timer set to record Survivor. I set another timer to record Life With Bonnie, which conflicted with Survivor, even though the two shows are on different days. A day later I tried to reset Bonnie, hoping that maybe the new guide download might have changed things. Well, it worked, sort of. I went to the Timer Management menu and scrolled through the events I had set to record and found that LWB was set as a one time only recording. When I edited it to record weekly... there it was - timer conflict with Survivor. I reset LWB to once only and, again, it didn't conflict.
Try to set one of your conflicting timers to once only and see if it works for you. Then please report here if it works. This'll have to do until the software is sent to correct it.