It turns out that the ASL software for encoding the ttl code received from DirectRT in the eye data file requires that the ttl code be sent out as a pulse. Leaving the ttl code on the port for any period of time, even 10 msec, results in it not being recorded by the ASL software. This is why the I/O TTL test worked (it sends a pulse), but my input file and the sample sendTTL input file did not work (both had time values for the ttl code set to 10 msec). I do not know why this is the case but it is. So, when the time value is set 0, there are no problems and the ttl code is recorded in the ASL eye data file.
Scott