Upon creating a sub theme, the theme name folder gets capitalized if your Human readable name is capitalized. The folder name should be the machine name, and not the Human name. For instance, if the Human readable name is Frak, then the folder will be Frak. If the Human readable name is frak, then the folder is frak. It is not anything crucial, but it is rather bothersome.

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DamienMcKenna’s picture

DamienMcKenna
Location NH, USA
CreditAttribution: DamienMcKenna commented
Status: Active » Closed (cannot reproduce)

Here's a command I just ran:
drush omega-subtheme --base=my_theme "My Theme Alt"

It created a clone of the my_theme theme with the project name "my_theme_alt". This is how it should be, if you're seeing something different please provide more details, i.e. the full Drush command you ran.