Good tips from 512k there. Especially the one about keeping colour counts to a minimum.
To explain why it happens: Bobs are nice but they have to be drawn by the blitter. So although the blitter can splat them onto the screen pretty fast, it's never going to match the speed of sprites. When you add in double-buffering to stop the flicker and a 32 colour screen (5 bit planes) the blitter has to draw bobs and replace backgrounds at a phenomenal rate. The images have to be drawn on each bit plane, so the more bit planes you use the slower it will be. As soon as you get to more than a few bobs on screen, the redrawing and checking for collisions takes longer than a vertical blank. So at the start, the game runs slower because one or more vertical blanks pass by before the next frame synchronises with a vertical blank. As the bobs get blown away, less time is taken doing the work and less vertical blanks get 'missed'. So the game speeds up.
So I would only add "Have you considered using AMOS's computed sprites instead of bobs for the enemies?"
Don't be put off by the term "computed sprites" as they're still really the Amiga's 8 hardware sprites. They're just broken into smaller chunks to make full use of a hardware sprite's maximum height which is 270 lines. That would never fit on a 256 line screen, just a quirk of the hardware. Still it gives you lots of moveable sprites at full sprite speed. You can use a 16 colour screen (4 bit planes) and have the remaining 16 colours of the 32 colour palette for your sprites. I won't go into the details of how you do it in AMOS as the manual has some good info on it in the whole of Section 7 (and look at the example help programs too). And it would be shooting in the dark without knowing exactly what you're trying to achieve.
Also consider AMAL to move your objects as it make any vertical blank timing and skipping dead easy with the
Update Every VerticalBlanks command. So if you need everything synchronised to 3 vertical blanks between each frame,
Update Every 3 does it in one simple instruction.
Maybe a bob for the plane and sprites for the enemies?
Good to see someone getting stuck into some AMOS programming
.