I had the same issue. But, I tried with the same program; It's working fine.
My experimental details include:
RT PCR plate - Applied biosciences
Sealer - Biorad
RT thermocycler - Eppendorf realplex
I have used all conditions and program same except for the reporter dye (Eva Green instead of Sybr Green), I results are quit promising and I found no issue.
Note: Since, I didn't use plate, thermocycler and sealer from same company. I first conditioned the machine for my plate and sealer, for which I added 10 micro litre milli Q water (depending upon your reaction) and condition the machine for plates and sealer placing plates in normal and reverse the plate and condition again. The results will be showed whether all wells can be read by the machine or not. In my case 3 wells in F row didn't work. So, I left the F row and reaction was performed in other wells. If most of the wells didn't work try to use correct plate for the machine...
For your question; definitely you can use same program for both reporter dyes...