Jay, we have 3 Zimmatics but they are all 25+ years old and have a different panel and probably different tower boxes.  Easily 90% of electrical problems have been microswitches but your problem does not sound like a failing microswitch.  We had a stall timer that periodically would not catch/reset, causing a shutdown; another time we had a loose wire in the control panel.  Adding capacitors (??) to the microswitches helped immensely on their life, but they still fail far too often.

With our style of panel and tower boxes, if we were to intermittenly lose power to the percent timer (if not dropped due to misalignment or similar issue), that would be a panel/power issue, not a tower issue.  If you said, I missed whether or not the forward or reverse contactor was dropped at the same time as the percent time lost power.

If you know the percent timer is intermittenly lossing power that probably means you are working with the panel open and live.  BE CAREFUL! (you know that or you would not be posting here!)

When our units run at 50% but not at a slower rate, I would check to see that all tower shutdown microswitches are properly centered in the cam when the alignment microswitches are camed in their proper working range.  Sometimes the arm on the microswitch needs to be bent to align them properly.  (Edit - actually this would be the fix for the pivot not running properly at a high percentage rate.)

 I would also look to see that the stall timer is not hanging and is functioning properly: sometimes the style of stall timer we have wear out or the screws loosen, allowing the clutch to slip.