Did your watch have the red jewels when you originally bought it? Given the timing of your purchase, and the fact that the clear ones were apparently introduced with the FM model, I presume it must have.
Looking at the Antiquorum pictures (see below), the watch now clearly has the clear jewels (pun intended)! Should we take this to mean that if an older RM 005 watch is sent in for service, RM will replace the jewels with clear ones, either as part of the standard work or perhaps upon request?

Picture from Antiquorum web site