That warning should be in Bold type. If you have the workspace hidden and do anything (load, etc) to the workspace, the blocks are corrupted and there really isn't much you can do to fix it. The problem stems from calls to
getComputedTextLength() and Neil attempted to do a bit of a fix to the problem in:
https://code.google.com/p/blockly/issues/detail?id=248. However, it only partially masks the problem. What there needs to be is a mechanism to temporarily hide the workspace (i.e. treat it as headless) and then once you unhide it, have the workspace go through and forcefully re-render everything. Setting the workspace to headless doesn't work because when you attempt to make it non-headless, the blocks are all derived from the wrong base block.