Well, I don’t know R very well, and I’ve never used the streamR package in particular, but according to the documentation for the parseTweets function that I just read:
The total number of tweets that are parsed might be lower than the number of lines in the file or object that contains the tweets because blank lines, deletion notices, and incomplete tweets are ignored.
If you want to know more, you will probably have to ask the author of the project for more help (unless anyone else here on our forums can help you)