Strobe lights, my guess is that;
your JAA country where you failed can do very little to get your current medical, issued by another state, revoked. If you have been issued with a medical certificate they really can't revoke it on grounds that were known when it was issued. Besides, another JAA member state has as little authority over other JAA states as you and me.
The country where you failed your medical could theoretically invalidate your (future?) flying licence when exercising the priviliges on aircraft registered in that country or, which is even more far out, prohibit you to fly in their airspace. I would say that the first example is against the EU principle of accepting each other certificates (especially since both are JAR) if both countries involved are an EU/EEA member. The second example should be against the ICAO convention since you meet the minimum standard outlayed by ICAO.
So in short, you should have now problem even though the country where you failed might give you a legal challenge in the future. However, do they require that you tell them that you use your JAR licence on their aircraft? If not, they will probably never find out and hence no probalem.