add a spell checker
On OS X, we'd use the built-in spell checker. For Windows, we're looking at several options, and are currently leaning towards hunspell, an open-source project with support for several languages. The Open Office project also uses hunspell.
I agree that this shouldn't be always-on. Many of the vocalizations I transcribe are not bonafide words from the dictionary, so red blotches could really get annoying. I find that a once-through after the transcript is complete is good enough for me (my current work practice is to copy the entire transcript into Pages.app, spot typos underlined in red & fix them, then copy and paste to replace the original text in Inqscribe.app).
I would want spell check to NOT be an automatic thing (like the red underlines in Word, etc). Part of what makes Inqscribe great, and has made transcription nicer, is not being reminded that I make a lot of typos!)