I temporarily uninstalled CSDM, and the problem is still there so that's not it.
My specs should be more than enough to handle it but here it is anyways:
P4 2.8 GHz CPU
1GB RDRAM
320 GB HD
Windows XP Pro
Nvidia GeForce 7600 GS
EDIT: like I said in my first post, the higher the values of cl_timeout and sv_timeout, the longer the problem takes to occur. The thing is, the cvars have a cap on how high they can go before resetting to their default values. Would a plugin be able to modify those cvars so that they have unlimited capacity?