It sounds like there could be two issues giving you problems. One is that the splice might be TOO tight. A proper splice will be flexible (somewhat, anyways) but still be plenty secure. Now, the glued ends could be the real issue - causing the spot where the ends are to be thick and unflexible, but also could be "slippery" where the glue is. Now, the other thing that the glue can possibly be doing is keeping the the rest of the splice from flexing since the glue is basically "holding onto" the ends and making a fixed point... as opposed to regular ends where they would flex and even pull into the splice a bit. Which, talking about "pulling in"... that's perfectly fine if they pull in a bit - they strength of a splice comes not from the ends "holding tight", but instead the entire length of the spliced ends woven back through and the friction/tension that is created as the line is pulled. Think of "Chinese handcuffs".
Now, if it was me, I would just cut the splice off and redo it - making sure to taper the splice. Since you're not comfortable with splicing, there are two (inexpensive) options that I can think of. One, check around the marina - invariably, there's gotta be someone there that knows how to splice. If not, check local marine stores for that service. Second, learn how to splice - buy some rope to practice with and practice at home. New England Ropes has a pretty good "how to" (look for something called a 'back splice' or 'chain splice').
You mentioned that the rope is fairly new and pliable so that shouldn't be the issue. However, a couple times a year I wash my rope (especially for the boats that have windlasses) right in the anchor locker. And then, once in a while (once every year or two) I remove it (or plug the locker drains, depending on the boat) and soak it in water with fabric softener added. Also, buying 'premium' rope helps quite a bit, too.
As a side note, and this has nothing to do with anything you're doing, it's a shame that your locker is too small to be able to handle the amount of rode you have - which is by no means excessive. I added a windlass to my Sea Ray Sundancer (28') and I have 50' of chain and 300' of line (pretty much the same as you) and there are absolutely NO issues with the line falling into the locker. The 'fall" distance is a bit over 36" and the floor is very wide, too (another 36" at the back and a bit less than that fore and aft). A boat the size of the Marlin should definitely have a bigger locker - or at least from what you're saying, it sounds like it's on the small side, anyways.
