Most likely it's a mod which is preventing you from getting the 5x multiplier, but which mod(s) is/are the culprits I couldn't tell you.
A mod could prevent you from getting the multiplier you expect in a couple of different ways:
1. By changing the governing attributes of certain skills, and/or
2. By changing the bonus multipliers in the game settings.
You can double-check the governing attribute of a skill by hovering the pointer over the skill in the character menu, which brings up the box describing the skill along with its governing attribute.
Checking for changed game settings is trickier. If you're familiar with the Construction Set you can fire it up, select a mod, and hit the "Details" button to bring up a list of the things the mod changes. Look for any changed game settings (GMST's); the game settings in question are iLevelUp01Mult, iLevelUp02Mult, iLevelUp03Mult, ... iLevelUp10Mult. The default values are as follows:
If any of these values are different then the bonus multipliers will not be the same as those listed in the article you linked to.
Another, more tedious, method of finding the culprit(s) would be to start a vanilla game with no mods, start a new character, level the character up "efficiently", and check to make sure the bonus multiplier is what it should be. (If not, there's something
very wrong.) Then add mods one at a time, starting a new character and leveling them up each time to see if the multipliers are still as expected; if not, the last mod added is the culprit.
I
can rule out the following mods as being the culprits, since I run with them myself and am familiar with them:
In addition, I would rule out any other official Bethesda plugins. The rest? Well, most of them don't
look like they would mess with the game in this manner, but not being familiar with them I can't comment definitively either way.
The only other thing I know is that the vanilla
unpatched version of the game
does not count miscellaneous skills towards the level-up bonus, but this shouldn't be the cause of your problem since you have the GOTY version which comes with the latest official patch by default.
I know this probably wasn't the answer you were hoping for, but I hope that it provides some help and insight on what might be going on here.