It's been awhile since I used an Amiga (I had a 500/600/CDTV in the early 90s)... and when it's booting, the screen is "blank" (and black) until the Workbench comes up ready to go... shouldn't I see some sort of outline of a WB window or something while it boots?
Mine does this also, I noticed it after I upgraded the ROMs to 3.1, so I presumed it was that. If you have something in User-startup (or startup-sequence) that outputs text, then the CLI windows appears before WB loads (the way it used to).
-Jar.