One reason it worked well then and now doesn't, is automation. Automated master control can be frame accurate, meaning if the switching between program elements can be perfect, as it is basically the same as a non-linear edit decision list. If the prep is done so that the last frame of a program segment is still in video and and the first frame of a commercial element is also in video, the commercial removal system will have no cue, as it usually keys on a few frames of black/silence. Most automation prep is done by placing a frame of black at start of message and end of message, so that there is at least some psychological separation that helps the viewer distinguish between two program elements, but a frame or two is usually not enough for a removal system to do the same.
By contrast, non-automated master control contained a lot of slop, since it is based on an operator pressing a button at a strategic time, and usually a sequence of buttons to dead-roll VTRs and then "take" them on a switcher. Regular fades to and from black with 5 or more frames of black in between program elements was extremely common, and nearly unavoidable. And manual master control is going the way of the blacksmith and the typewriter.
Another reason is the trend of commercial lengths being quite varied compared to broadcasting a few years ago, and automation has helped lead into this as well. 10 years ago most commercials and promos were 30 seconds long. Now, many still are, but many are not. Since the early removal systems keyed on not just fade to black with silence, but their algorithm also included another criteria--that the fades had to happen between 28 and 32 seconds apart--these days that criteria is only met about half the time reducing the accuracy rate.
The Replay system was much more sophisticated and worked quite well, but it angered the powers that be and helped hasten Replay's demise as a contender on the PVR scene. They removed the feature a couple years ago, but by then the damage had been done.