I haven't heard of maany problems like your's, chap, but I think I can help ye' a little.
There ain't much I can do but advise ya'. I woul recomend checking if the cfg. files for markings and items are in the FH main folder, unless you don't want them to appear.
If you try and reinstall feralheart, make sure everything that came with it is deleted with it, not a bite of FH on your system. (If you want though you may preserve files for maps and such, but not the folders that they are in. for example exports and stuff)
Also are you sure the two downloads are compatible together, will they work fine against each other?
Like rocks in real life, some game downloads rub each other away and create small errors, grains of sand that soon spread and become a large error to the game system.
All I can say is that ye' download them again or find help from other users. Sorry if I didn't help ya'.