Promotions revisited

I found something last night in Rodenbough's The Army of the United States that I'd never seen and am not sure I understand. It was on page 203, in the 3rd US Cavalry history section.

"In consequence of the retirement of Colonel Simonson, September 16, 1861, Marshall S. Howe was promoted colonel of the regiment under the new system, which , however, did not repeal the law which made promotion lineal in the regiment. But appeal and protest were alike in vain."

LtCol Howe was promoted and assigned from the 2nd US Cavalry, where he'd served as second in command to Col Philip St. George Cooke since 1858. The new system that is referred to is the renumbering of the regiments in August 1861. It's the "law which made promotion lineal within the regiment" part that I'm unsure about. I've found several instances of promotion across regiments prior to the Civil War, generally as lieutenants and occasionally as captains or majors. Perhaps there was a tradition or law that regimental commanders were promoted from within the regiment. Howe, for instance, had served for ten years in the 2nd as a major, prior to promotion to LtCol in 1858. I doubt this would have been practical at the beginning of the war, as some regiments (the 5th US, for example) were literally decapitated.