I've seen FreePPP do this a lot when my ISP upgraded their 3Com servers, and mostly with v.34.
When you look at what shows, esp. if it is an initial authentication error, the host is sending out a long Welcome message that seems to confuse FreePPP direct dial. A script works because it knows what promts (not a CCL script - look in a terminal window to see what is happening).
It was so bad I switched to LinkUPPP! which never had trouble (allows for secondary authentication, turning on PAP and/or CHAP). Switched ISP to one that was "friendlier" (the original ISP only had problems with Macs and with FreePPP or with 33.6k modems - which cleared up after months of throwing new modem servers and updates).
Remote Access 8.6 seems fine with v.90. Hopefully 9.0 will improve internet connections - can't be having a reputation as troublesome with internet can we! (Even if the problem is with 3Com host modem servers or something!)