SQLite has a reputation of being small, fast and flexible. I used it in one of my C++ projects to save simple statistics to a file. Once for 15 minutes 3-5 new simple records (5 rows of integers) were saved into the database. During few weeks of such SQLite usage I quickly observed clearly noticeable disk usage. I wasn’t expecting that, because amount of data written was very small. If I would write it to a plain text file a reaction of the disk would be hardly noticeable. Is SQLite really such light database, or was my problem too simple for use of a relational database?
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VACUUM may solve your problem. http://www.sqlite.org/lang_vacuum.html