Weird junction problem

Hey everyone, this is my first post on the forum - I hope someone here will be able to help me out.

I recently bought an SSD and in order to conserve space on the drive, I did a fresh install of Windows 7 and created junctions for the "Program Files", "Program Files (x86)", "Users", and "ProgramData" directories that pointed to a second (D:\) hard drive.

For the first couple of days, everything looked perfect - an inspection of C:\ under Windows 7 would report the correct amount of used/free space. However, now the drive is reporting an INCORRECT amount of used/free space. For some reason, I believe it is including the space in my junction shortcuts as local used space.

I am not sure if Windows Update has somehow caused this problem, but I would like to correct it if I can.

So far all I have tried to fix it was rebooting into the administrator account, using the command prompt to perform a rmdir on the junction folders on C:\, and then re-applying the mklink command to re-create the junctions. However, that did not solve the problem.

I think I should also mention that the junctions are working as intended and everything (I've tested this by placing test files in the junction folder and making sure they pop up in the corresponding D:\ folder and by deleting the files and checking vice-versa). This is just the problem of Windows reporting the wrong amount of used space on the C:\ drive.

I used this method to perform the junction creations during my fresh install (again, I had no issues):
Windows 7 Move the Users and Program Files Directories To A Different Partition | Tuts4Tech

Thanks in advance to anyone who can help me figure this out!

I'm going to go ahead and post some images for clarification purposes:

Here's a screenshot of "My Computer":
http://a.imageshack.us/img210/2408/computeri.png

Here's a screenshot of my "C:\" drive, with junctions setup:
http://a.imageshack.us/img836/9921/89305354.png

Here's a screenshot of my "D:\" drive, where the junctions are re-directing to:
http://a.imageshack.us/img801/7913/96097497.png

Here's a screenshot of my "D:\" drive folders, showing their true used space:
http://a.imageshack.us/img827/5538/dspace.png

Here's a screenshot of my "C:\" drive, reporting the same used space:
http://a.imageshack.us/img844/4053/cspacejunction.png

Here's a screenshot of my "C:\" drive, showing what the true used space SHOULD be:
http://a.imageshack.us/img841/3851/cspacetrue.png

As you can see from the pictures, the C:\ is reporting that 29.5 gigs are in use, when really it should only be reporting that 22.7-22.9 gigs should be in use.

(Also, I do have "Show hidden files, folders, and drives" checked under folder options in Windows Explorer.)

What you are doing in the last picture of getting file size is always going to be incorrect.
The values listed in Drive Properties on my Computer is always correct.

It is not adding the junction points to the number. Because the way Drive Properties gets the free and used space is from the hard drive bitmap which contains every single bit the HDD can hold, and every single bit that is currently in use. Always accurate always correct. If the bitmap isn't correct, there will be problems, extensive horrible problems.