So, I was doing a 12 Endings w/saves run utilizing the quicksave feature (F6) and was having a wonderful time saving about a minute and a half until I got to the Apartment Ending.

I quicksaved right as the lights turned on for the phone and picked up the phone after it was done saving. Once I was in the apartment, the narrator did his speech as normal, but the prompts for keyboard presses did not show up. I was able to advance the dialog by smashing all the keys on my keyboard, but eventually even that did not work.

I then pressed escape, which brought up a key prompt instead of pausing. Hitting the prompted key made the appropriate noise, but did not advance the story. Hitting escape paused the game after that. Additionally, quicksaving and then loading did not advance the dialog either.

tl;dr: Quicksaving may mess up the Apartment Ending, effectively ruining any run that uses it before picking up the phone. More testing soon.

Yeah, I tried a run doing the same thing, yet came upon a big issue right around there. What happened to me was that it didn't say anything for about 20 seconds, gave me a key prompt, and then went along regularly. I still saved time, but haven't bothered to submit because I wanted a sub-57 before submitting. I'll try to find the point in the VOD though.

There is a fix! So, I did some testing, and I believe the quicksave popup is what causes the glitch. To circumvent this issue, just hit the escape key before the first key prompt comes up. Instead of pausing, it will fix the glitch and continue like normal.

In my testing, I found that quicksaving in-between key prompts would reinstate the glitch, which could be fixed again by trying to pause the game.