For installing software packages, long delay in recognizing startup disk

I have found that any time I install software using an installer package (e.g. flip4mac) on my iMac, there is a long delay before my startup disk is recognized as a valid installation location. All of the other drives are evaluated immediately, but I'd say it's about 20 seconds before I get the option of my startup disk (green arrow pointing down at a picture of a hard drive).
Does anyone know what is causing this and how I might alleviate the problem? It's annoying, and I wonder if it's a sign of some deeper problem.
I do have a bootcamp partition that I rarely use, and I have an external USB drive that I use for time machine backups.

The more external storage devices you have connected to your computer the longer it's going to take to for your computer to evaluate which volumes it can install on. Short of dismounting the external HD's first this is the price you will be paying for all the external devices. BTW I'm in the same boat, I have 3 EHD's daisy chained together using FW 800.

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