To me this looks like a timing problem in your software. I believe that you clear the receive flag and may be the interrupt request flag in your receive interrupt routine. At some point you execute this routine to process receive byte n, and during this process the UART receives already data byte n+1. In this case clearing the interrupt flag inside the receive routine will delete the interrupt request for n+1. It may be that some other routine in your software blocks the receive interrupt too long to always run the receive routine before the next byte has been received.
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