Please read all before doing anything!
Test the surface temps of each strip on each level. And be sure each is exactly the same. If fact, this is where you should start.
This is a very tough question to answer by not seeing the unit and guessing at electrical issues.
1 I doubt a crimping problem. Mainly because if it was, it would be due to a resistance caused by a bad crimp on the lower temp areas. I doubt this because the wattage is so low in flexwatt the resistance would have to be very very low (yes a possibility) but it would also be steady (also possible) but I just don't think this is the issue.
Here's the way I would test this.
Electrically:
You will need a multimeter, and know how to use it to proceed.
Test voltages at the other end of each flexwatt on the copper outer strips. DO NOT do this if you are not fully confident in your electrician abilities. I tell you to do the ends sjust in case there is a rare case that the copper leads along the outer edges of the FW has a crack in it. I have seem damaged FW mainly due to storage. And you never said if it was new old or what ever.
If voltages are different then it may well be a crimping issue.
Voltages should probably fluctuate with movement of the crimps. Temperature variations would also, but would be so slow to react to the voltage and near impossible to detect.
If voltages are stables then:
Unplug the unit.
Now if each strip connected together in parallel you need to isolate each strip. The check the resistance of each strip.
maybe it's the strips?
My guess is the way you are connecting the temps and maybe there is different heat losses at each level. I do believe the surface temp is much higher than 110?
Test the surface temps of each strip on each level. And be sure each is exactly the same. If fact, this is where you should start. So I will paste this also at the beginning.
Good luck and please be careful.