That very well may be a false positive. Like the warning message says, it is common for a capture to start in the middle of a tcp session. In those cases it does not have that information. If you are really missing acks then it is time to start looking upstream from your host for where they are disappearing. It is possible that tshark can not keep up with the data and so it is dropping some metrics. At the end of your capture it will tell you if the "kernel dropped packet" and how many. By default tshark disables dns lookup, tcpdump does not. If you use tcpdump you need to pass in the "-n" switch. If you are having a disk IO issue then you can do something like write to memory /dev/shm. BUT be careful because if your captures get very large then you can cause your machine to start swapping.
My bet is that you have some very long running tcp sessions and when you start your capture you are simply missing some parts of the tcp session due to that. Having said that, here are some of the things that I have seen cause duplicate/missing acks.