When using the various /weather commands, the effects on the weather cycle differ depending on which command is used. This is very difficult to observe directly in a given world, but is easier to see in the level.dat file.

Steps to reproduce:

1. Create a new world
2. Upon leaving the world, note the NBT data for the rain and thunder time. This is the default for starting a new world, and what one might expect when the weather cycle resets.
3. Reenter the world and use /weather clear (with no duration argument)
4. Note that the clear weather duration in this case is much less than the default, and that the rain and thunder times are fixed at 1.
5. Reenter the world and use /weather rain 1
6. Note that the rain time seems to be reset normally but the thunder time is less than normal.
7. Reenter the world and use /weather thunder 1
8. Note that the rain and thunder times are even longer than when first opening the world (likely the default)

Attachment notes:

First screenshot: New world
Second Screenshot: /weather clear
Third Screenshot: /weather rain 1
Fourth Screenshot: /weather thunder 1