I know that the vram in Mac mini in some cases dont get recognized as 64Mb, but only 32Mb.
This happens here if I boot straight into MorphOS. But if I boot with holding the Alt key and select MosrhOS I always get full 64Mb.

Normally I never notice any difference, if its 32 or 64 Mb.
But now I just changed my monitor, so now I have 1680x1050 as my default resolution. Now I notice some smalll graphical errors that probably is because of lack of vram.
When I boot direct and get 32Mb the background colour on the PolyNet NG dock is black, and it refuses to go transparent. Same goes for the backgroung on the mouseeyes module.
If I boot with the Alt key and get 64Mb, the backgorunds are transparent like they should be.

This is to be fixed in MorphOS 2.5 I have read. But is there a quick fix available for it at this moment, so I can get 64Mb even if I boot MOS directly?

No, the MOS team has no time to release hotfix type things like this apparently, MOS 2.5 is on the way so expect a change soon.

There's no quick fix, unfortunately. A temporary workaround is to reduce memory usage by switching to 16 bit mode instead of 32 bits, and/or switching off enhanced layers for Ambient screen, until 2.5.

> A temporary workaround is to reduce memory usage by switching to 16 bit mode
> instead of 32 bits, and/or switching off enhanced layers for Ambient screen

As temporary workaround I find it much more convenient to boot MorphOS via boot menu :-)

I tried to set the workbench to 16 bit mode. That does fix the transparent colour for the PolyNet dock, but the mouse eyes still gets black background. (no big problem, I just disable the mouseeyes anyway)
But in 16 bit mode, my E-Uae workbench colour gets rather ugly. So I guess my best option is to use the Alt key for now.

I was just hoping there was a way to do something on the mac side (in the startup scrips).

For the moment the only fix is to hold alt key when booting, as you mentioned anyway. Hopefully new MorphOS will come soon.