Companion Bug

[TGCX45]

So I've been having a problem with Fallout 3 companions recently. Whenever I dismiss them, I still keep their companion perk. For example I still have Charon's "the contract" perk and Fawke's "over-compensation" perk. I also tested it with Star-Paladin Cross and I permanently have her "Second Skin" perk now as well. And I also can't recruit any non-humanoid companion anymore, as when I try to recruit ED-E, he says that he can't come along because Dogmeat is following me.

The problem with that is that Dogmeat was dismissed when I reached a certain point in quest (I think it was when I was kidnapped by the Enclave in vault 87), and whenever I talk to him I can't get him to follow me again. The only dialogue option I have is to say goodbye. I even killed Dogmeat and ED-E still acts like Dogmeat is still following me.

Here is my load order:

FalloutNV.esm
DeadMoney.esm
HonestHearts.esm
OldWorldBlues.esm
LonesomeRoad.esm
GunRunnersArsenal.esm
Fallout3.esm
Anchorage.esm
ThePitt.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm
CaravanPack.esm
ClassicPack.esm
MercenaryPack.esm
TribalPack.esm
TaleOfTwoWastelands.esm
YUPTTW.esm
AWorldOfPain(Preview).esm
AWOPDeadMoney.esm
AWorldOfPainFO3.esm
Functional Post Game Ending.esm
TTWInteriors_Core.esm
TTWInteriorsProject_Combo.esm
TTWInt_FollowerGoHome.esm
AnotherInteriorMod.esm
Regulators.esm
A Trail of Crumbs.esm
AWOPDeadMoneyVendorPatch.esp
TTW - AWOPNV.esp
TTW-AWOPNV-AWOPFO3.esp
Functional Post Game Ending - AWOP Patch.esp
TTWInt_FPGE_Patch.esp
The Mod Configuration Menu.esp
LootMenu.esp
CPI Icons.esp
JIP MiniMap.esp
FOVSlider.esp
Diagonal movement.esp
B42Inertia.esp
JustAssortedMods.esp
Conelrad 640-1240.esp
R.A.C.E. Station.esp

[Laclongquan]

Have you tried
1. Using companion dismissal panel in megaton craterside supply
2. Take a boat ride to point look out
3. Take a trip to the pitt.
4. Travel to the strip, lucky 38 casino, take a elevator to presidential suit (your suite) then back out

[TGCX45]

I used the Companion Dismissal terminal and I'm am now able to recruit Dogmeat and ED-E again! Thanks for the help, I'm a little embarassed that I couldn't think of that myself.

For some reason I'm still keeping the companion perks after dismissing them though. I'm not sure how to even go about solving that other then manually removing them via the console every time I dismiss them. Any suggestions would be greatly appreciated