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I'm on v1.41 and 3.10a firmware 

Ok. I will upgrade my core and hardware. I am on 1.29 and 3.7.  One last question: Rogue64 is dependent upon using the SID function for random number generation. Could it be that you have an ArmSID or some such SID replacement in you U64 that doesn't have the SID rng function? If so, could you try disabling the SID sockets and see if that helps? 🙂

Hello, I don't have any SID's inserted, I'm just using the built in FPGA SID and only 1 of them. I did however reinstall the 3.10a update and sure enough, the game works now! 

Ah. Very good! I just upgraded to 1.41 and 3.10a on my U64, and the game works fine, so I was getting worried it might be something else. Excellent that you figured it out! 😎