Are you using the latest version of Web Essentials 2012? (2.0 at time of writing) And of TypeScript (0.8.1.1)? I had the same issue with an earlier combination of WE and TS 0.8.1, but it was fixed in a recent release.
WebEssentials can be configured either to compile on save, and/or on build. Go Tools > Options > Web Essentials > TypeScript
in VS2012 and try toggling these switches and see if this helps.
Disable Web Essentials, go to the Tools > Options
as described above, and try turning off Compile TypeScript on save
. This way you can have all the benefits of WE without the performance hit
Update
WE 2012 has just ticked over to the next version: 2.1