We've observed the same behaviour, in our case the cause was the tailing process does duplication detection with a checksum on the first and last 256 bytes of a file (so as to not index the same file twice).
We had two files with identical content being monitored.
Our resolution was to use crcSalt = A and crcSalt = B in each stanza which ensured they had differing checksums (we could do this because the duplicate files were listed in two different monitor stanzas).
You should also beware of changing the crcSalt on a running system as it will cause previously indexed files to be re-indexed.
Over a 10 minute window our splunkd.log looked like;
INFO WatchedFile - Will begin reading at offset=1575 for file='/tmp/logtest/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=1890 for file='/tmp/logtest/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=2115 for file='/tmp/logtest/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=2205 for file='/tmp/logtset/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=2340 for file='/tmp/logtset/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=2700 for file='/tmp/logtset/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=2970 for file='/tmp/logtest/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=5490 for file='/tmp/logtest/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=6795 for file='/tmp/logtest/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=7560 for file='/tmp/logtest/test_2013101419.log'.
INFO WatchedFile - Will begin reading at offset=9810 for file='/tmp/logtset/test_2013101419.log'.
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