HP360 color inconsistencies lately

We've been having some strange issues with our HP360. We're using Flexi Production Manager RIP..
Co-worker exported a batch of files as pdf (raster and vector elements). Prints are good but one of the prints gets ruined during installation. Export the 1 re-print as a pdf same as before and now the raster image prints with a different shade around it. The raster image is a transparent png on a blue sign. The blue behind the transparent image is slightly lighter than the blue background of the sign. Had no problems printing the first go around but every print after would fail. Absolutely no change in profile or setup.
Couple of days later I send a batch of signs (raster & vector mix) as pdf. Same issue. One transparent raster image has a background color shift. I had to use a powerclip/clipping mask to get the "transparent" image to print without a background color shift.
A week later we send a batch of prints that need to match a specific pantone color. We first send a test print with vector only pantone filled squares. Comes out a near perfect match to our pantone swatch book. So I ensure the same pantone is used in the sign to be printed. Yes, the signs have both raster and vector elements. Export as pdf using the exact same settings. Now the same pantone vector elements are way out. I ended up rasterizing the whole bit as CMYK and got the job out. The pantone were slightly different but "close enough" I chalk that up to the RIP converting the cmyk to CMYKLcLm

p.s. RIP, Flexi, was recently updated to latest version about 3 weeks ago. That's what I blame but....

 

Test print 1 = vector square with pantone fill - exported as pdf
Test print 2 - vector sq w/pantone & transparent png/tif on blue background.
Test 1 is perfect
test 2 vector pantone is way out & transparent raster image has a background color shift.

 

blue background is cmyk vector, pantone colored square, and transparent rgb png. Best way we've found to match pantone colors would be to use pdf.

 

Yes, that's what my solution was. Except no need to "flatten" the png or convert to jpg. Just powerclip into a circle. - still a workaround not an acceptable fix
What about the pantone color shift? No reason for it to change just because raster images are thrown in the mix.
And yes, my theory was that the transparent raster images weren't mixing well with vector backgrounds. Still doesn't explain why it worked the first go around.