From my limited experience there could be charges and a considerable delay in receiving cleared funds; it will depend on what bank the cheque is drawn on.
If the cheque is drawn on one of the Irish Clearing Banks then it will be no problem, however, if the cheque is drawn on a Continental European bank (eg Deutsche Bank / BBVA / Rabobank etc etc) it will need to be sent for value on a "collection" basis.
Because there is no centralised European Clearing system what happens is that your receiving bank send the cheque for value from the issuing bank - ie they effectively cash it themselves - once they receive the money they then lodge it to your account. Bank of Ireland used to charge for this; I'm not sure if they still do.
I recently sent a euro cheque to a UK company, Expansys.ie (I had received assurances that they had a euro denominated account; it turns out they have but they don't use it!!) - it took three weeks for the funds to clear as they cheque was sent for "collection".
Despite the additional cost I reckon it would be much easier and faster for ETrade to SWIFT the money to your Irish bank account rather than send a cheque.
There are other AAMers that use ETrade - maybe they could advise on charges and timings for payments from ETrade