So what you need to do is: go to media toolbox .
Select you'r amigaos4 bootpartition and click add, remove or edit filesystems.
Click add and select the filesystem you are using on you'r bootpartition (i hope you are using smartfilesystem?) ? the filesystems are located in L: btw. and the dostype is 53465300.
Save the changes and now you hopefully should be able to boot from you'r os4bootpartition.