However, it would appear the issue had to do with the player becoming invisible after getting out of the chair in the Memory Den during one of the quests (Dangerous Minds?) and not the general chameleon and stealth boy perma-invisibility glitch which patch 1.5.4 introduced for many players. The Steam Beta patch notes mention “Fixed occasional issue where player would become permanently invisible”. I don’t plan on upgrading to level 5, since I know the 1.6 Patch is going to cause issues when it is released for Xbox One. Fortunately although I play Fallout 4 on Xbox One, my Sneak Perk is only at level 4. So, you have to use another mod to enable them. However if you are playing on PC and are on Survival difficulty, Console commands are apparently disabled. If you are on PC, there is a console command that will allow you to remove just level 5 of Sneak. This is apparently triggering the chameleon / stealth boy perma-invisibility glitch on PC.

The first is that level 5 of the Sneak Perk is being changed to include a brief chameleon effect.

Bethesda has apparently made 2 changes with the 1.6 Patch that were not good.

Fallout 4 .45 pistol mod