I think modern guilt may be beck attempting to cry out for help from scientology, read some of these lyrics;

I feel uptight when I walk in the city
I feel so cold when I'm at home
Feels like everything's starting to hit me
I lost bed ten minutes ago

-Many Scientologist have experienced intense feelings of paranoia, brought on by the institutionalized belief that the world is against scientology.

Modern guilt I'm under lock and key

-Frequently when scientologist inciate members into their higher levels, they will begin a period of forced isolation.

As for the term, "Modern Guilt."-

[Modern Guilt], Don't know what I've done but I feel ashamed

-Another scientology ritual has the aim to induce intense loyalty, which involves getting the subject to admit to things they have done in the past, and crimes which they didnt even comit.

These people talk about impossible things
And I'm falling down the conversations

-Few Scientologist who may be rushed into heirarchal registration find the advanced beliefs very difficult to believe. This is because scientology is designed to break down your resistance to new and new beliefs over time.

Modern guilt is all in our hands
Modern guilt won't get me to bed
Say what you will
Smoking my cigarette
Don't know what I've done but I feel afraid

-Easy enough, Beck may be feeling that scientology is a mixed up and made up religion, and that he is very stressed about losing his life to it further. As he was born into it, he may feel that he had no other option but scientology.

I hope you get better Beck, that maybe you break out of this cults hold! I want you to know that their are alternatives and that you should feel safe.