Could it be overprint/transparency settings being double applied? This is one that snags us every once in a while in Illustrator for both vectors and rasters, process or spot.
I should probably elaborate on this. This is not intended to be a thread hijack.
Simply put, an object in illustrator assigned transparency: multiply and fill: overprint will cause problems but it gets way more complex than that and this is what I am going to explain. This can be maddening when going to a RIP but typically occurred upon generating a PDF. This is possibly a very confusing explanation but it's the best that I can do. I'll post a screen recording if requested.
Illustrator treats layers/sublayers/objects basically the same. It's a little known feature and rarely used on purpose. The typical use is accidental and occurs when using the Layers panel "Select all objects on layer" button (the circle at the right side of a layer label). It's a quick way to select only the objects on a layer but instead of selecting the objects like a selection drag with the selection tool (Black pointer) it actually selects the layer. Thus when you apply transparency effects or overprint settings with this selection technique the effect/setting is not being applied at the object level but at the layer level. If you select just the layer in the layer panel you won't see the transparency and overprint. You'll only see if you use the "Select all objects on layer" button (the circle at the right side of a layer label). This also allows you (why!?!?!) to assign effects/settings on the sublayer, group, subgroup and object levels creating a dual effect/setting.
Therefore, an object can actually have per level transparency and overprint settings which can really confuse the hell out of a RIP. I have seen crazy color shifts on objects because of this.
Side note: if you select all, copy/paste and paste into a new document (with or without paste remembers layers enabled) the layer level effects/settings are not carried over which typically eliminates the problem. We used to file this under a "corrupt document" explanation until I finally figured it out.
The first time I finally figured it out the job was a carton produced: Opaque White (2 hits) + CMYK + Varnish + Spot Coating + Emboss. As a believer and practitioner of composite files my press file had a diecut layer, emboss layer, coating layer, varnish layer, trap layer, opaque white layer 1, opaque white layer 2, then various artwork layers. That's 7 layers on top of the document with transparency/overprint settings. The CMYK artwork was shifting upon generation of a PDF as if a Photoshop adjustment layer for curve had been applied at 30% to output 50%. It turned out to be the scenario described above with the Opaque White layers/objects.
