Ernie has a point about environment. Besides the time of day and sunlight issues, are there any CCFL lights in ANY of the rooms the IR sensors are located. Just 1 florescent light shining on an IR sensor that is not designed for it, could cause problems in the whole system. Although usually it would affect the OEM remotes too - but still possible.
To that point, the TV's = How old are they? If they are LCD and CCFL backlit, there is a huge source of florescent light right there. Any of the TV's plasma? - major problem light source for most IR systems.

Also what brand of IR receivers you are using can help as well. Big difference between using a Xantech DL95 and some generic POS off of amazon.com. Some of the cheaper (well most of the cheaper) IR systems are known to have problems.

Adding: How you tried to learn the codes in matters as well. If you did it standing in front of a plasma TV or LCD w/CCFL back light, that is guaranteed to corrupt the IR learning. Also near any CCFL lights will do it.
You should always try and shield the IR window of the learning remote, from any light source when learning codes. Also play with the distance and method of pushing the buttons (feathering, push & hold, tap, etc...).