I've had the same issue with bottles left to soak more than a couple days. A very quick hit (a minute or two) with Lime-A-Way or similar fixed everything.
Primary: , Boddington's Clone, Mirror Pond w/Marris Otter
Bottled: Fullers ESB Clone
Kegged: Mirror Pond Clone
Drinking: BM's Kona Fire Rock, Dead Guy Clone, Alaskan Amber Alt Clone, Firestone DBA Clone, Magnum/Crystal IPA
Next up: Burton IPA