Hi,
You can look at the transistor sort of like two diodes with one common junction. That common junction changes the behavior from simple diodes to a transistor. However, when you bias the junctions individually one at a time like you did (and this is a common practice just to perform a quick check on the transistor) you can look at it as two separate and distinct diodes. When you look at it in this light, you see two diodes that are constructed somewhat differently and this means their operating parameter values are different. For example, the emission constant is usually different for both diodes as well as the saturation current. The result is that for the same forward test current each diode will measure a different forward voltage.
Im sure you already know that to perform a better test you should test it with a forward base emitter current and a reverse base collector voltage.