Of course, if you were using the OLG1 inside the case with the provided GPS antenna, that would be a problem. You are getting the Red LED and the Yellow LED? You must be getting the Yellow LED associated with data if the U3S is receiving info from 4-sats... You might have a solder bridge on the U3S that is preventing the 1PPS line from changing state. That would fit with the observed situation that 3oo3 kits now are not working for you. 

Lastly, if you are going to use an external antenna that is connected via an SMA connector to the OLG1 rather than the included antenna, then you must  install the optional L1 and R1. As I recall, the solder pad of L1 closest to the SMA connector location on the board, needs to be connected to the center pin of the SMA connector. If you don't do that, your external antenna is not going to be powered, and it will not provide a signal to the board.

73 KJ4VPI. Sam