And until some one comes up with a more complete explanation and concrete evidence (none of which currently exist), there is no proof Alexei suffered from anything other than hemophilia.
This isn't concrete evidence, but an explanation:
It would be nice if it was that clear cut, but to this day in the 21st century a proven diagnosis does not exist. The puzzlement is that Alexei had a few symptoms that hæmophilia simply cannot answer.
One of the most convincing was that Alexei's disease was episodic. He went months, and even a whole year without any problems worth writing home about. Hæmophilia is ever present, the body lacks the clotting factor it needs for the blood, making every injury dangerous. Alexei rumbled, tumbled, stubbed his toes, got his fingers caught, and endured many other childhood bruises.. but not all of them haemhorraged. He wasn't fighting for his life with every stumble.
Take a look at every serious attack, and it is noted that Alexei was generally feeling under the weather along side the bleeding problem. Each time his immune system was down, say with a cold, he seemed at further risk of reacting badly to an injury. His temperature would rise, saying that his body was very plainly trying to fight off an infection of some kind. Extremely high fevers led to delerium, a trait of the Central Nervous System.
None of this is consistant with hæmophilia.
The greatest mystery was the fact that sometimes Alexei's attacks would occur some time after the initial injury. A perfect example is the Spala Episode, it took weeks for that attack to fully flare after his accident in the boat. In laymen's terms, hæmophilia just doesn't do that. That disease acts right upon the injury, it doesn't fester for weeks.
Nor does a hæmophiliac attack suddenly disapate as quickly as it begins. Alexei's recovery in 1912 was quite spontaneous. The results were temporary crippling, but he was well on the road to recovery only a few hours from when it seemed all was lost.
All of the symptoms seen in the Spala case, the pallor, internal haemorrhaging, high fevers, and delirium match with what medical science now calls Aplastic Crisis. In Aplastic patients a virus, like a common cold, compromises the bone marrow's ability to produce healthy red blood cells. An injury then could be potentially fatal. It is also a self-limiting disorder, meaning that as soon as the infection runs its course the crisis is over. An Aplastic Crisis episode will last anywhere around six to ten days and then subside all on its own. The recommended treatment is to give the patient comfort and support only until the infection is gone and the marrow is able to recover.