You are 100% correct... the M39 is a 1st generation pistol. It is also the single stack mag pistol and the holster for it will not fit the double stack mag 5906 & 659.
I like to use a Safariland 568 "custom fit" paddle holster (
Model 568 Concealment Custom Fit Holster w/ Molded Paddle :: HOLSTERS.com) for my pistols, there is enough "give" where it will fit many pistols with the same general frame/slide/barrel length.
I f you don't care for a paddle, it comes with a adapter to make it a belt loop holster.
I can carry my S&W 4006 & 559, and my Glock 22, in the same model holster. I also have one that fits my 4506-1 and PC 945 pistols.
As you can see, it's also adjustable for retention.