Can't create SSIS package from Import and Export Wizard
We are using SQL Server 2012 SP3 [11.0.6020.0] Enterprise Edition and SSMS 2014 [12.0.4100.1] and have the same issue.

The pictures below are: 


SSMS version
Import/Export Wizard complaining about edition
Result of @@version showing Enterprise Edition


Since at work I had SQL Server 2008 R2 SP1 Enterprise Edition [10.50.2500.0] + SSMS RTM [10.50.1600.1] (they just applied SP1 on server only, all clients remained RTM) I know 100% this couple was working fine.
I patched my Studio so it then became 10.50.6000.34 and this couple: SQL Server 2008 SP3 + SSMS SP3 was still working fine.
At home I use both the server and the studio patched, i.e. both of them [10.50.6000.34] and this configuration also has no issue.

Then the Server at work migrated: all the dbs were moved onto SQL Server 2012 SP3 that is shown on the picture [11.0.6020.0], for sure Enterprise Edition, we are using partitioning...And here came a surprise: our clients have the new SSMS 2014 [12.0.4100.1] installed, and the Wizard does not save the packages anymore!
That was the first time I see the bizard complaining about Edition.
So I was wondered if it's a known issue or no and I googled it up. I found no workarounds or explanaitions but I did found the Connect Item

Using Enterprise Edition; Can't Save SSIS Package from IMPORT WIZARD

Status : 

Closed
  as Not Reproducible  Not Reproducible

So I just concluded it's a bug that won't be fixed  (ok. because we cannot give any reproducible scenario), but it's just there

I had no chance to test your version [10.50.4000.0] and tis is the first time I read that the issue persisted on 2008 R2. I thought it was SSMS 2014's bug