Brand guidelines vs usability
Brand guidelines assure that a company is consistently presented across various media and formats. What's problematic, however, is when these guidelines don't take into account special requirements of certain new media, eg. a branded web application header.
Assume the brand guidelines state that the minimum size of a logo should be 100px high. Now that might be ok for a promotional website (based on which these guidelines were probably created), but has great implications if used within browser-based software that staff use on a daily basis.
Slapping your brand name in the header of an application is a bit like the Power Point disease of 'stamping' each of your slides. If our memory lasts longer than a few seconds, we know that we're dealing with company xyz!
But what's annoying and distracting in a Power Point creates serious usability issues within a browser. 100px or more of a vertical browser resolution of sometimes no more than 500px is over 20% dead space! If users have to scroll down every time to reveal important information below the 'fold' (and some of these users don't have scroll wheels), you'll be wasting huge amounts of time and money in the long run.
Consider this scary calculation: 3 seconds for each scrolling action, performed 1000 times by 1000 employees every day is 3 million seconds, or 833 hours, or more than 1 month lost every day!
So for the next brand guidelines revision, why not invite over some user interface experts for tea and save your company a fortune in the process.