My recommendation is to use 32-bit bitwise operations instead of using unrestricted bitwise operations, or to operate on 64 bits worth of data instead of 32 bits at a time.
As you don't show any code, it is hard to give any more concrete advice. Please post a Short, Self Contained, Correct (Compilable), Example so we can see what the cause for your problem might be and suggest appropriate remedies or workarounds.
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