After moving my project from my development machine (Windows) to my web server (Linux) I ran into the common tablename issue because Windows makes all tablenames lowercase. I fixed this by modifying my dump file and replacing all the tablenames with proper TableName schema Silver Stripe uses.

Anyways, after doing that the site worked fine.

Now there are duplicates of each table in the db. For example: sitetree and SiteTree

However, after adding new page templates and running /build/dev/ i get the following error:

[User Error] Couldn't run query: ALTER TABLE "SiteTree" ADD "HomepageForDomain" varchar(100) character set utf8 collate utf8_general_ci, CHANGE "ClassName" "ClassName" enum('SiteTree','Page','Forum','ForumHolder','ArticleHolder','ArticlePage','ContactPage','HomePage','ErrorPage','RedirectorPage','VirtualPage') character set utf8 collate utf8_general_ci default 'SiteTree' Duplicate column name 'HomepageForDomain'

I have all the proper permissions to alter the table so permissions arent the issue.

It seems for whatever reason it is trying to create a duplicate column name "HomepageForDomain" in the SiteTree table.

What the hell is going on?

This is almost definately a windows -> linux problem

The best thing to do is just make a dump of your windows DB, import it to linux, apply the patch (linked below) and it should be all fine.

See this patch:
http://open.silverstripe.org/ticket/2476#comment:2

One other thing I would try is this.
Back up your database.
Then delete the column name HomepageForDomain, that is causing a conflict.
Then try dev build again.