I had met a same problem, and could not resolve it.
I just import data into H2 (embeded mode) through jdbc in first time, and following I will only execute jdbc query, but the *.mv.db file size auto increased dramatically, from about 600M to 1.8G, if query without "union all", the db file size will increase to 1.1G.
I need a help, why this happen and is it will affect the performance?