If I got straight, you had a .TS file from which you removed the commercials.
I don't know for sure for BD, but on DVDs, these clips will always be non seamless, unless authored into a single file. It may be the same for BD. In that case, the LG made you a favour while the Panny was stricter.
There is another possible problem - the discontinuity of the time code stamps (at cuts). Try running the file/s again through tsmuxer to provide a continuous TC.
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Born in the USB (not USA)
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