Currently, if you use the stock one and two button dialog VIs in your code, they will block the root loop while being displayed.
For those of you who don't know what the 'root loop' is, this is the core process of LabVIEW that many UI functions must execute under. One of the key functions that executes in the root loop is VI Server calls to open a new dynamic VI. So, if your code has multiple threads all performing operations that involve dynamic calls to other 'plug-in' VIs and one part of your code calls one of these stock dialog VIs, then all the other threads will be blocked until the user clears the dialog.
As a result of this, I have had to write my own 'root loop safe' versions of these dialogs to prevent this from happening.
As a side note, dropping down a menu and leaving it down without selecting anything also blocks the root loop. It would be great if they could fix this too!