Makaron has no HLE to boot games, it's only through execution of the BIOS code that games are being loaded. With that in mind if your BIOS or FLASH file are damaged or corrupted, many games will not boot at all or BIOS will freeze trying to load them.
Make sure you have correct time & date settings in the Dreamcast BIOS. This is very important. If it keeps asking you to set those every time you run Makaron it's not good.
To enter BIOS do not set any game images, or set an unbootable one. There is one BIOS I'm aware of that will freeze anyway - you can trick it by setting a GDI image and wrong region so it will not boot.
Follow the procedure in ReadMe.txt file. With sepearate FLASH files you'll need to do that for each region of course