Agents can belong to two and be active in two splits at the same time.
If you do a 'display capacity' command, you'll find that there are two measures of agent login licenses. One is Logged-In ACD Agents, and the other is CMS Measured ACD Members. Both are important here. If you only have 100 of each, then you can only have each agent in one group at a time (assuming that you have 100 active agents).
You might also want to check the number agents that were setup in the CMS for data storage. (If you have one.)
In the R5, I think that the limit for active agent membership was 4 groups simultaneously. (It went to 20 in R6.)
You generally have to program two sets of control buttons on each agent station. AUX, ACW, and AUTO-IN buttons have to be duplicated for each split the agent will be a member of, otherwise the agent has no real control, and can't be in the auto in mode to receive calls. FAC's can do the job, but it makes leaving a group hard, since you have to get a dial tone to enter an FAC, and that's not so easy to do in busy call centers.
The login process must be repeated for each split the agent will join. (Dial tone, login FAC, split numb, agent ID, release, dial tone, login FAC, split numb, agent ID, release.)
You might do a 'status station xxxx' and check the lower left hand part of the screen. (xxxx would be the agents station number) You should see a listing of the hunt groups the agent is a member of, and their current state in that group. If the agent is a member of both, then it should say so.
If you're using non-eas splits, make sure you remembered to list the station as a hunt group member for BOTH groups. Do a 'change hunt-group xx' and check for the agent station to be listed in both places.
Carpe dialem! (Seize the line!)