I've just installed windows on a friends PC, which is using an SSD for Windows and core apps (Photoshop etc), and a standard HDD for less critical apps and data.
To do this, I installed windows on the SSD, then used junctions to move the users & program data directories to the other HDD, which is working fine. However, in order to be able to run some apps from the SSD, but most from the HDD, I left the Program Files directories on the SSD, and created new directories on the HDD which I instructed Windows to use as default. This doesn't seem to be the right move, as nearly all Windows apps (photo viewer etc) are now having problems, and some things aren't installing right.
Is there some way to link the two directories together, so that C:\Program Files will also have links to D:\Program Files, or should I be doing something completely different to fix this?