There are a number of possibilities here.
First is to check the computer’s event logs to see if there are any indications of problems reported there.
Another is that something is acting on the files, slowing the directory read. As examples, AV and spyware detecting software can cause this.
In the case of AV software, configure the software to exclude either the file extension(s), or the parent directory, or just disable it briefly, and see if that makes a difference.
In the case of spyware detecting software, temporarily (at least) shut off the drivers for the software. As example, both Ad Aware and Spyware Doctor use drivers which run from about the time the computer starts up. I've seen many cases where these programs and other similar programs can create problems similar to what you describe. The drivers for these programs can be changed from automatic startup to manual or disabled. This is done in Computer Management under Services. For the test, set them to disabled and also stop the service(s).
Another experiment is to just open the suspect folder in windows explorer. If its slow there, it might indicate drive related problems.
You can also use Window’s task manager to see what, if any processes increase their CPU time when Photoshop does a directory read. In this case try opening a couple of folders containing a lot of data to see if the problem follows or is specific to one or more locations.
There are a number of web sites that have software to run drive diagnostics. Best is to find out the manufacturer of the drive and go to their web site and use their recommendation for drive diagnostic tools.
Before you do anything, perform a full backup...