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?