I would have to see your configuration to say, but it sounds like you've either enabled "Use FTL Modifiers" or "Hold" on a mapped key that should not have this enabled.

To add Shift+1 through Shift+= to the default 1 through =, all you have to do is follow WoW Quick Start Guide: Quickly add many hotkeys, optionally with auto-assist. Many New Mapped Keys, right in the FTL DPS Keys, as shown in the screenshot is perfect.