Two things that might relate to what you are experiencing:
(1) There are what I like to call 12-controller Sound ROMS and 16-controller Sound ROMS, meaning the factory presets on those ROMS were designed primarily for 12-controller 1 rack unit boxes (Proteus 2000, XL-1, etc.) or for 16-controller boxes, such as the Command Stations and Proteus 2500 (and I assume the keyboard models). The operating systems for 16-controller boxes have more [virtual] patchcord sources and patchcord destinations than 12-controller boxes. That accounts for some things that might behave differently.
For example, the XL-1 ROM aka XLEAD is a 12-controller ROM and the factory presets do not use the additional 4 patchcord sources--MidiM , MidiN, MidiO, MidiP--as well as the 4 additional Continuous Controllers (CCs) assignment coming from external midi sources, initial CC amounts coming from presets, etc.
[more on this later]
(2) So far as I have read (and seen on a few ROMS), the use of controller assignments in factory presets--virtual patch cords--are not used exactly the same across different ROMS. For example, from what I have read, the B-3 ROM uses controllers and patchcord assignments very differently than say the P2000 Composer ROM or the XLEAD ROM.
In addition to the above, later Sound ROMS added additional resources, such as arp patterns and RIFFs. So although the original Proteus 2000 ROM (aka CMPSR) has the same sound samples as the P2500 ROM (aka P2500), there are BTS (beats) RIFFs and arp patterns on the P2500 ROM which are not on the CMPSR ROM.
So, the factory presets for the Command Stations and P2500 have controllers directed towards various arp functions. If you put a 12-controller CMPSR ROM in a P2500, I suspect the bottom row of knobs won't change anything (because on the CMPSR ROM, the factory presets do not have patchcords with assignments for MidiM -> MidiP.
However, you can always assign patchcords to anything you want via the User presets.
Sean Wilhemsen of E-Mu was kind enough to create and make available banks of 16-controller presets for User ROM that were designed for 12-controller ROMS to be used in 16-controller boxes. So, if you have the XLEAD ROM (designed for the XL-1 and XL-1 turbo, 12-controller boxes) the controller assignments will not be the same as an XL-7 ROM, even though the sound samples and mulisamples are the same.
But if you upload Sean's 16-controller presets for the XLEAD ROM, you will have knob assignments comparable to the the XL-7 ROM. However, you won't have the additional RIFFs that the XL-7 ROM has.
I'll have to look, but I think Sean also made available a set of MP banks so people could use the the original 12-controller Mo' Phatt ROM in 16 controller boxes.
I am not sure of the differences you were talking about, but if its the ones I describe, I hope the explanation helps. If its something else, feel free to describe those differences.
Steve