Difficult to see how the same version could be installed twice if presumably you accepted the default install location for it. The second installation would simply over-write the first one -- so you still end up with only one copy of it installed. More likely Windows has simply logged it (in error) as two copies in "Add/Remove Programs". One of those entries needs removing, but not by running it's uninstaller. This would remove the actual program and you don't want to do that. All you want to do is remove the entry.
The list in Add/Remove is maintained in the Windows Registry, under a key labelled 'Uninstal', but I don't advise you to go messing with that. Much safer and easier is to download and install Piriform's 'Ccleaner' from here: http://www.ccleaner.com/
1. Start Ccleaner and click the 'Tools' icon
2. Highlight one of the entries for 'Net Framework 1.1' (either one is okay), then click 'Delete entry'