Luc,
I'm not sure our experience parallels yours, but when we had intermittent differences between our front and rear air conditioning it was due to differences in the settings of the two thermostats. (In our case it was the rear air conditioner that would start, run for a couple of minutes then shut off -- in 104 temps in Arizona.)
The major suggestion that I got was to make sure that both the front and rear thermostats are set to exactly the same configuration. You can have separate temps, but all the other settings must match. I found differences, made them both the same and everything has worked just fine since.
Hopefully, your situation is similar and can be fixed just as easily.
Bob
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2003 Beaver Patriot
2014 Honda CRV Toad
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