I believe there is a forever loop in one of the test cases. Specifically the case:

[
mov a 5,
inc a,
dec a,
dec a,
jnz a -1,
inc a,
mov a -10,
mov b a,
inc a,
dec b,
jnz a -2,
mov a 1,
mov b 1,
mov c 0,
mov d 26,
jnz c 2,
jnz 1 5,
mov c 7,
inc d,
dec c,
jnz c -2,
mov c a,
inc a,
dec b,
jnz b -2,
mov b c,
dec d,
jnz d -6,
mov c 18,
mov d 11,
inc a,
dec d,
jnz d -2,
dec c,
jnz c -5,
]

On line 7 reg b gets its initial value of -9 from reg a. On line 10 it is decremented to -10. It is then decremented 8 more times. When I get to line 24 reg b is -18 so it has me go back 2 where it has me decrement it again to -19. By the time it overflows the Int32 to get back to 0 it has timed out.

Did I miss anything?

I like how you combined both the encode and decode into one method. Very clean. Nicely done!

Something is wrong. When I run my solution in Visual Studio it takes 12,000 ticks. 1 millisecond = 1000 ticks. Why does it take more than 12,000 milliseconds (12,000,000 ticks) to run the same code here? I believe I have a solution but it times out. This is frustrating.