Could be a power problem. If you try to power both the HDD and the CD drive from the original A1200 power supply, then the first access to the CD drive might cause a power failure.
Nevertheless you should try the following: edit s:startup-sequence and remove the first few lines which were added by the IDEfix installer (comments and C:IDEfix). Move them to another text file so that you remember them to put them back later.
Also move CD0 from Devs/DosDrivers to Storage/DosDrivers. (There might already be another CD0 in Storage/DosDrivers. Rename that one to CD0_old or simply delete it. You only need the new one.)
Then boot up with the CD drive connected. When Workbench is fully loaded, open a Shell window and enter IDEfix.
If it does not crash, open Storage/DosDrivers and double click CD0.
If IDEfix crashes, try CD0 anyway. If CD0 does not crash, try to move it back to Devs/DosDrivers. If the CD drive is the only reason why you use IDEfix, then you can leave startup-sequence as it is and only use CD0.
If neither IDEfix nor CD0 crash when run manually, it might be a timing problem. Try to run CD0 from WBStartup instead of Devs/DosDrivers.
Also run Prefs/IDEfixPrefs and check if it complains about invalid settings. If it does, then correct the settings it complains about. Do the same with Prefs/CDFSPrefs.
Also try to change the settings in IDEfixPrefs which are set to "auto". Change them to match your hardware. Maybe automatic detection does not work.
BTW, how big is your boot partition ? The Amiga can only boot from partitions which are completely inside the first 4GB of the HDD. And then you have to load additional drivers to access the area outside the first 4GB.
Bye,
Thomas