After a lot of searching I determined the source of the problem and provided a fix in 0.4.2-beta. The Exchange extension should not cause new negative balances any more when matching trades. The bug was partly due to differences in the application of maker and taker fees to the base currency while buying the quote currency. If you wish to continue testing the plugin, I would suggest that you first wipe all trades and orders from the database, with delete from wp_wallets_txs where category='trade';delete from wp_wallets_orders;
I will keep the extension in beta for a short while longer and if no more bugs are detected, it will be bumped to 1.0.0 (i.e. production-ready).