My cd copy of GR is scratched beyond use so I downloaded the one off ubi and when I Went to Instal my island Thunder disc it says "Ghost Recon must be installed before installing Island Thunder. Exiting Insall now."

Has anyone had this problem/have a solution?

hmm. maybe you have a 1.4 patched CD witha a non 1.4 patched Ghost recon 1/desert siege?
Otherwise try to install ghost recon and desert siege first, and after that install island thunder.
My CD was scratched, i downloaded an illegal version (oops) installed it but didn't install the crack, and my scratched c'd works to let the game start (so I effectively used only the data package that was broken due to the scratch) I didn't want to pay for a new CD with handling costs and such.....