Some Lugers are picky about ammo... It doesn't take much of a difference either.
If both rounds are using the same weight FMJ bullets, there may have been a change in powder type or some other difference. Different powder may develop the same muzzle velocity, but with a different pressure curve.
Lugers cycle in a rather fine tuned balanced way. Dirt can impact cycling, but I am assuming your gun is clean and properly lubricated - especially since it doesn't misbehave when you go back to the original ammo.
After trying another magazine (which is good advice, since it's easy to damage a wood bottom magazine) the next thing to do would be to ensure that the extractor well is clean and then consider changing the recoil spring. Use a lower power spring (they are available in sets). The 7.65mm Luger round develops slightly less recoil than the 9mm, and the pulse shape is different.
While you have the extractor out, check to verify that the face of the extractor hook has not been damaged in any way.
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 Igitur si vis pacem, para bellum -
- Therefore if you want peace, prepare for war.
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