The Pathfinder, or "3.5++", Control Weather strongly implies that the effect is stationary and is explicitly stated as centered on the caster's position for a two mile (three mile for Druids) radius (4 mi/6 mi diameter).
Moreover, PF states: "You change the weather in the local area." I believe this is additive to the centered on caster and makes the effect explicitly stationary.
Though the GM may always allow some interpretation, as @Pellanor suggested. I certainly would not say "No." Instead, maybe a "Yes, but... you must make a Will Save or other concentration save, should the caster cross half the radius in overland/sea movement, to move the spells area of effect (at an appropriate DC accounting for lapses concentration or possible interruptions)."
Update The BECMI spell from the Rules Compendium, Weather Control reads very differently than Pathfinder. Specifically, there is no Control Weather spell and the Area of Effect and duration are both significantly limited in size and by caster focus. Additionally, the spell allows specifically for movement with the caster:
This spell allows the magic-user to create one special weather condition in the surrounding area (within a 240 yard radius). The spell caster may select the weather condition. The spell only works outdoors, and the weather will affect all creatures in the area (including the caster). The effects last as long as the spellcaster concentrates, without moving; if the caster is being moved (for example, aboard a ship), the effect moves also.
The "select[ed]... weather condition" includes the following on sea-borne casting:
High Winds: No missile fire or flying is possible. Movement reduced to half normal. At sea, ships sailing with the wind move 50% faster. In the desert, high winds create a sandstorm, for half normal movement and 20' visibility.
This finding effectively invalidates my below thoughts on "bring science to the table" however in context of how the spell has evolved and how it is cited to work in 3.5 and Pathfinder, it is still valid. YMMV.
Considering the purpose of the spell in context, to move a ship and not lose "puff," the GM should probably rule on this, possibly accounting for prevailing weather in the area. If the science were at play, the area of high pressure and temperature differentials created by the caster, thus moving the air from a high to low pressure zone, may move with the prevailing winds outside the area of effect.
Combining elements of both rules for a house ruling appears to be an acceptable option. Various "retro-clones" of OD&D simply allow for significant GM fait... sorry, discretion in range, duration, and by absence, mobility.