I suspect your different results are due to your differing warm-up routines. If I'm doing an FTP test then I need a good solid 20 mins of progressive warm-up time and I need to be feeling reasonably fresh. The Gold standard test on SYSTM is the "Full Frontal" 4DP test, but it is brutal! I've done both several times and had consistent results between them for FTP. As you might expect, the ramp test has more chance of throwing up an odd result. But it's less painful to perform and you don't need to be quite so fresh. On the SYSTM forum many users report that the ramp test tends to over-estimate their FTP, but for me it has been pretty accurate (relative to the 4DP test).
I presume your room temperature and cooling fans etc were all set up the same for both tests?