The boot.ini file which can be found by doing the following:
Run>Msconfig>Boot tab - will show you the 2 installations. On my PC it shows the following text:
"Windows 7 Professional (C:\Windows) : Current OS; Default OS"
What I assume you have done is you let Windows make the ~100MB System Partition + move the old data to the Windows.old folder , when doing this (sometimes it has happened when making a clone of a faulty drive) I have found the end result is sometimes the issue you are having.
To correct it, please post a ScreenShot / link to a screenshot of your "Boot" tab under Msconfig, and I can advise you from there on which one to delete (but they both work so they might be exact copies of each other).
ZK
EDIT: What I do to avoid this is when installing Windows, to Delete ALL partitions, then click Next, Windows will then use the free space as 1 single partition. Downside is you will need to clone the drive/copy the data off before hand and copy it back, which isnt effective, from a time POV.