The intelligence officers from the different services only spend a few years with these joint intelligence organizations, and are still plugged into the intelligence organization they grow up in. To no one's surprise, each service has different words and procedures for the same intelligence task. Efforts are made to get everyone using the same terms and methods, but the army guy will often find it convenient to get in touch with his old army intelligence buddies if he has a problem to solve. Getting down with the air force or navy guy (or, quite often in the intel business, gal) in the next cubicle requires more effort. Moreover, if an intelligence officer uncovers some particularly interesting information, from the perspective of his service, he may spend additional time working on it with people from his own service, before sharing it with the officers from the other services. This is a good career move, as it means a better chance of getting a pat on the back from his service's intelligence brass.
As a result of all this, there is a major problem with the intel officers from the different services not appreciating how important something is to the other services. Being on a joint staff is supposed to teach that, but what often happens is that everyone grinds out the analysis as if they were still working just for their own service. Much effort is then required of senior officers to go over these reports and try to see which service has been slighted. But often it's difficult to do this, as an army officer will frequently just ignore stuff that doesn't register with a ground combat officer, but could be of vital importance to the navy.
The basic problem with "jointness" is that it is temporary. This has been pointed out for years. But the obvious solution, to set up an organization that takes in officers as lieutenants and let them spend their entire careers in "joint" organizations, has never been accepted by the different services. So the senior intelligence people on these joint staffs just grit their teeth and prepare to herd cats for a few years.
The United States Department of Defense is running into problems getting the different services to cooperate on intelligence matters. The major commands (like CENTCOM, which controls operations in the Middle East and Afghanistan) use officers from all the services to form the intelligence staff. Makes sense, as this way you get different perspectives. But in practice is has been causing confusion and more inter-service conflicts. The most immediate problem is the different intelligence perspectives and needs of the different services, especially the navy. This is because the navy operates on land, air and on the water. Moreover, naval intelligence officers regularly ship out as part of fleet or task force staff and have more experience with the sailors and ships that do the fighting than do their army and air force counterparts have with their fighting troops. The army and air force intelligence officers tend to be more into the high-tech type intel (satellite and electronic) than the navy and marine intel officers. None of this was unknown when the joint intelligence staffs were put together, but the different services have not blended as well as was hoped.