I have no idea if it relates to what you describe with cask and
dependencies, but I had the same error and found several old threads
stating that it's caused by installing org when it's already initialized.

I solved it by Emacs -q and reinstalling from elpa. If you search for the
old threads there was a link to documentation that explains why this occurs
which may be of some help addressing with cask.
On Jun 17, 2014 3:38 PM, "Grant Rettke" <gcr@wisdomandwonder.com> wrote:

> Good afternoon,
>
> Just upgraded to 8.2.7 and was surprised to get the
> "org-with-silent-modifications" error. Here is what happened.
>
> The first time that I set up my Emacs libraries, using Cask, which
> uses the Emacs package manager, it install org2blog which has org
> 8.2.6 as a dependency. Then, Cask installed org-plus-contrib 8.2.6 and
> life went on. Then I can cask update to get the 8.2.7 release (Cask
> just pulls from the org repo).
>
> Started up Emacs and got that aforementioned error. The issue seemed
> to revolve around load-path or
> load-order, and I didn't understand any further than that. It was very
> strange because my whole approach
> had been to automate everything so it would "just work".
>
> Poking around, I eventually saw that org2blog depends on "org" (yes
> now I admit that I didn't know this when
> at first, but that is not relevant here I believe). That just didn't
> look right to have both orgs in there, so I deleted plain old "org"
> and commented out the org2blog load. Now Emacs works again.
>
> The issue seems to be that org-plus-contrib doesn't satisfy "org" from
> a package manager perspective.
>
> This surprised me because the former is a superset.
>
> My next step now is to figure out what to do from a package
> perspective, because I would like to keep
> org2blog in there.
>
> Anyone else encountered this and want to share the solution?
>
> I'm going to think about this some more and see.
>
> Kind regards,
>
> Grant Rettke | AAAS, ACM, ASA, FSF, IEEE, SIAM, Sigma Xi
> gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/
> “Wisdom begins in wonder.” --Socrates
> ((λ (x) (x x)) (λ (x) (x x)))
> “Life has become immeasurably better since I have been forced to stop
> taking it seriously.” --Thompson
>
>