Your MD5 sums for the VP (i.e. retail game data files) look OK to me:
Tthe root_fs2.vp seems to have the problematic mission SM1-07.fs2.
I've also just tried playing Slaying Ravana from the tech room (on Linux as well) and the Cyclops is correctly appearing in my loadout. Could you please try playing from the tech room & report the results?
i.e. Tech Room -> Mission Simulator -> Select Campaign Missions -> Press CTRL-SHIFT-S (to see all missions in the campaign)
In the tech room simulator, I can load Cyclops in the weapons loadout screen (but it is not equipped by default). Using cyclops during simulated mission works as well.
I noticed that SM1-06.fs2 was not available as a simulation until I hit ctrl-shift-s. Should have it been, at this stage of the game?
I had a look at your pilots, unfortunately I can't test with them because you seem to have included files from two different pilots?
My mistake, sorry. I'll attach both files for both pilots in a couple of minutes.
I have extracted SM1-07.fs2 and loaded into Fred. It seems to indicate the Cyclops#short is available, but not Cyclops. Attached is screenshot:
[attachment eaten by a Shivan]