FYI: this Amiga is recapped with ceramic capacitors. But it didn't show this behaviour right after the recap. It has been about a year and a half in storage since.
Hope someone has an idea.
The first thing I would do is take off your hard drive and see if the delay is there with just booting a WB floppy. The delay could be an issue with the compact flash or HD controller.
Most important I would get that thing recapped properly. Ceramic caps in place of the proper ones are not in th design for a reason. Using them is not better! Get good high quality long hour under higher temps and they will last the lifetime of you using it.