Windows 7 HDD problems

I've experienced a strange problem with my Windows 7 performance and I'm some kind of stuck with it.

I have the following symptoms:

During the usage of some programs (e.g. Lightroom or Eclipse) they randomly stop and I'm not able to do anything
During these random stops I've seen that the free space on the HDD is reduced to almost nothing and after a while the free space grows up to its original value (Normal free space: 1.69TB/4TB, Stop free space: 312GB/4TB)
During the random stops, I'm not able to access the HDD via File Explorer, it seems like all access to the HDD is blocked somehow
The random stops have a duration from a few seconds up to 1 minute

What I've tried:

My first idea was that there must be an error on the HDD. However I've replaced the HDD in question with a brand new one but the problem still exists
I've checked the HDDs multiple times, there are ok
I've disabled the indexing service

As said after the stop everything works normal again until the next stop.

What could be the reason for these random stops? Any ideas?