I have constant freezes and enclave soldiers are for some reason invincible, YUCK. It usually crashes when I try to sae.

I also experienced the never ending loading screen.

[X] Fallout3.esm
[X] Anchorage.esm
[X] ThePitt.esm
[X] StreetLights.esm
[X] BrokenSteel.esm
[X] PointLookout.esm
[X] Zeta.esm
[X] iHUD.esm
[X] Impervious Power Armour.esm
[X] EVE.esm
[X] Apocalypse Armory.esm
[X] Mart's Mutant Mod.esm
[X] EnclaveCommander-NoFreeRide.esm
[X] GalaxyNewsRadio100[M].esp
[X] Existence2.0.esp
[X] Dree Perks.esp
[X] Dree Perks Anchorage.esp
[X] Dree Perks Pitts.esp
[X] Dree Perks Broken Steel.esp
[X] Dree Perks Point Lookout.esp
[X] Dree Perks Mothership Zeta.esp
[X] CrowdedCities_v2.esp
[X] NPCs Sleep Tighter.esp
[X] MiniHideout.esp
[X] Apocalypse Armory.esp
[X] Apocalypse Armory - DLC Enhancements.esp
[X] sunglassescollection.esp
[X] EVE.esp
[X] EVE Operation Anchorage.esp
[X] Apocalypse Armory + EVE.esp
[X] Mart's Mutant Mod.esp
[X] Mart's Mutant Mod - DLC Anchorage.esp
[X] Mart's Mutant Mod - DLC The Pitt.esp
[X] Mart's Mutant Mod - DLC Broken Steel.esp
[X] Mart's Mutant Mod - DLC Point Lookout.esp
[X] Mart's Mutant Mod - DLC Zeta.esp
[X] Mart's Mutant Mod - Hunting & Looting.esp
[X] dD - Enhanced Blood Main.esp
[X] Realistic Death Physics.esp
[X] Fellout-pipboylight.esp
[X] Fellout-Full.esp
[X] Fellout-Anchorage.esp
[X] Fellout-BrokenSteel.esp
[X] Fellout-PointLookout.esp
[X] Fellout-Zeta.esp

Not sure what is wrong? I patched to 1.07 and have the latest FOSE and everything got sorted by BOSS. Any help? I've tried everything but it keeps happening.

Well one problem, first of all, is that you do not have a Merged Patch. Try downloading FO3Edit, creating one, loading it last of all, then see if the problem remains.