Hmm, that’s odd… I’m getting the feeling that the embedded timestamp is in seconds, not milliseconds though? That being said, could there possibly be additional characters at the end of each line? Can you see NUL characters or something similar if you enable “Show control characters” under Display Options? I would expect at least CR and LF to show up which is to be expected, but we have seen NUL characters sneaking in on more than one occasion.
One UART change that went into the 2.5.0/2.5.1 software was that we wanted to make sure that the timestamp corresponds to the earliest character on the line, previously the software would take the last timestamp, which normally isn’t what is desired. In this case that “feature” might have masked a different issue. If a NUL character is trailing the LF after each line, that NUL character will end up on the next line and the corresponding (early) timestamp will follow it.
If you can share the otii project then we can take a closer look at how the UART data is structured.