From what I can ascertain from the OP, he has two moodle installs which are both using the same database, but without using different database prefixes.
This would mean (if this is indeed how the two installs are setup!) that there was one user table in the database being accessed by both moodles. Each time a new course was made in one moodle, it would also exist in the second moodle; as there would only be one course table... and so on... I can not see when this would ever be a setup that someone would really want, and by the sounds of it, this is not the setup the OP has. He states that users who access from URL 1 can not login if they visit URL 2. If this is the case then there must be two user tables, one for each URL; and therefore two databases...
In terms of the major difficulties I was hinting at, consider this:
one database with two moodles using a different database prefix (in essence two databases!) but sharing the same moodledata folder. How does the database distinguish which files belong to which Moodle? This is perhaps less of an issue with the Moodle 2 data directory but would have resulted in course files being shared in incorrect courses using the Moodle 1.9 data directory method...
Anyway, none of this really helps the OP, and unless Alan can provide a little more detail to how he has his two Moodles set up, I think we will continue to struggle to help! I would hazard a guess taht what we are looking at here is a need to migrate users from one Moodle to another a perhaps backup and restore courses from one to another too.