I took a train from Istanbul to Thessaloniki in April. Didn't experience any problems other than delays at both border sides because of rail traffic.
It is, however, a "real" border and not open like going from France to Germany. We had to stop when leaving Turkey and then again when entering Greece.
In Turkey you will be required to pay for your visa upon arrival IN YOUR NATIVE CURRENCY. I cannot stress enough how much time this will save you if you know this in advance! It was a major problem for me because I had just come from over a month in India with a few days in the UK, so I didn't have any dollars on me. They would NOT accept pounds (unless you're British) and they certainly wouldn't accept rupees.
It was a very stressful 20 minutes but it worked out in the end when one of the travel partners I'd met up with that day turned out to have some US dollars.
So yeah, the moral of the story is
make sure you carry some of your home country's cash before entering Turkey!!!