This was posted several years ago and I kept a copy....
All told there are a total of 7 R2LC's that were produced thus far.
They are as follows;
C04 (early modular TMCC locos and command ready modular boards)
C05 (used exclusively in the Lionel Backshop)
C06 (used in the later TMCC steamers (such as the later semi scale pacifics and hudsons, after the whole motherboard issues were corrected)
C07 (used initially in the C-420's only, but then used by licensees)
C08 (the most common, produced in the largest number, compatible with all aftermarket upgrade boards, this is the board pretty much everyone uses; Atlas O, 3rd Rail, Weaver, K-Line (even the new SD70MAC's!, etc. the C08 board is also the one that will be sent to anyone who orders an R2LC from either us or DD.)
C11 (used in newer RS 5.0 locos with Odyssey)
C13 (U33 now the most current R2LC, used in all new production Lionel stuff with RS 5.0 and Odyssey)
While I really cannot comment on the differences internally with the software I can tell you that there are some (a very few at that) C06 boards with tunerless pots in circulation. Most all C04's, C06 and C07's have tuner pots (shiny metal adjustable frequency potentiometers) that can easily come out of tune to the 455KHz TMCC frequency if bounced around in shipping, etc. There are some C07's, all C08's, C11's and C13's have tunerless pots, meaning they withstand the bounces in shipping and are fixed to the 455KHz frequency.
Early C04, C06 and C07 boards do not support the AUX1 + 8 feature in the program mode (to turn smoke on/off at 12VAC constant) the C08, C11 and C13's do support the AUX1 + 8 program feature.
Hope this helps sort out the differences.
