A SQL command times out online but not in app engine

We have two custom processes dealing with large amount of data, and they are basically doing the same thing. One of them kicks off the process via online, and the other does the same thing in batch App Engine process.
Recently, our online process stopped working with timeout error, but the batch process completes just fine.
We've located where the timeout is happening, and it was at a SQL command dealing with large amount of data. The online process uses ExecSQL() to run a script, and App Engine uses SQL action, and their scripts are identical. Aside from the fact that our table is growing bigger and bigger, which is causing timeout, is there a way to make online process work in the meantime? Is there a place we can configure timeout limit that works for ExecSQL()? What's making difference between running the same command from ExecSQL() and SQL action in App Engine