Maurizio84: yeah the harbor/ship system can be a pain in the ass sometimes especially when you have many of both.

you could try denying access to warehouses and hq from your soldiers so that they can enter only in harbors in every island and mainland and see if it helps, it is possible you'll have to block access from harbors to military structures by cutting some roads but i'd try the harbor thing first.

as far as i know the problem exists because after you played with the distribution settings soldier A was trying to from mainland to island B and to guardhouse C but something was blocking the way or they hadn't reached the designated building yet when you rolled back to defaults at which point they are still trying to reach their target but for example ships don't register the need to transport them anymore so they try to find an alternate route which ends up in your whole army walking around on an endless loop, or something like that...