There is another problem.
In place where should be the Join Item will stand, let the sword, then when you log on to the server it will disappear.

I'm having issues understanding what your trying to explain.
Is this what you mean? : In the place of where an ItemJoin item would be placed upon joining such as the ultra-item being the diamond sword, there is a non-itemjoin item in its place and ItemJoin is overwriting / removing the non-itemjoin item from my inventory to put the custom item in the inventory?

Yes!

The only way to prevent it is changing the slot # to slot: Arbitrary which puts the items in the first available slots.

There is an option in v4.0 that prevents items from being overwritten, but that wont be out until Wednesday or Thursday.

Merged with Issue #94