Noel Borthwick [Cakewalk]
Most likely CbB is receiving the sequence for a valid NRPN and therefore interpreting it as such. You could try looking at this in MIDIOx. I bet you will see it interpreted as a NRPN as well. You can also look at it in the event list view.
 
The convention of a pair of controllers being used to denote RPN's and NRPN's has been in the MIDI spec for decades and every version of Cakewalk has implemented it this way historically. 
 
I suppose there could be a preference to translate CC's to NRPN's but its not like were hijacking them. This is the official MIDI specification behavior.
 
 

Thanks for answering, Noel. I am just sending cc101 values to the synths, not the whole combo needed for an RPN value, so CbB just ignores it. If I manually enter the data, using any method in CbB, those values are also ignored and not sent out.

My point is exactly what Chris above says, it should be converted on destination, if applicable, not by CbB. All those synths I mentioned above, including Blofeld, use controller numbers 38 (OSC FM), 100 (Filter envelope release) and 101 (Amp Envelope Attack). This implementation makes it impossible to automate or remote control those parameters from CbB (or Sonar). Every other program capable of receiving midi that I have currently installed, including Rapture Pro standalone, recognize those cc numbers as controllers by themselves.

Many VST's are completely unaware of the MIDI spec as far as RPN's or NRPN's are concerned. I don't think in itself thats precedent for hosts to also ignore the MIDI spec however considering that MIDI pre-dates all these synths :) I think it was a poor choice for these synths to hardwire these controllers in the first place since they have a special meaning in MIDI.
I havent looked at the code but I assume that when you enter a RPN combo in Cakewalk we're internally using that as a trigger to identify the MIDI event as an RPN. 
 
I understand your point however.

I still have my Cakewalk 3.0 (MIDI only) installation files from '90-ties somewhere. Sometimes when working on more specific MIDI problems (like this above) in Sonar, I'm forced to go back to Cakewalk 3.0 to get the job done actually. Never let me down. The way it handles MIDI files always helped me solve the problems I otherwise had in Sonar. It's Event List is showing everything. I always did enter (N)RPN or MSB/LSB and Data Entry even SysEx messages manually there and it worked perfectly. For me it's foolproof when cleaning odd MIDI files or checking if there's something going on wrong or simply managing SysEx banks.