I believe it means not feeling well or up to par.

People on ships became seasick most often during times of rough seas and bad weather. Seasickness is caused by the constant rocking motion of the ship. Sick people would go below deck, which provides shelter from the weather and often would feel better down below or "under the weather". :P Richard Shines

Feeling under the weather: UNDER THE WEATHER - "Ik Marvel, a pseudonym that resulted from a misprinting of J.K. Marvel, was the pen name of American author Donald Grant Mitchell. In his 'Reveries of a Bachelor' (1850) Ik Marvel is the first to record 'under the weather,' which has been a synonym for everything from 'ill and indisposed' to 'financially embarrassed' and 'drunk,' and has even been a synonym for 'the discomfort accompanying menstruation." From "Encyclopedia of Word and Phrase Origins" by Robert Hendrickson (Facts on File, New York, 1997). To be under the weather is to be unwell. This comes again from a maritime source. In the old days, when a sailor was unwell, he was sent down below to help his recovery, under the deck and away from the weather. "Under the weather. To feel ill. Originally it meant to feel seasick or to be adversely affected by bad weather. The term is correctly 'under the weather bow' which is a gloomy prospect; the weather bow is the side upon which all the rotten weather is blowing." From "Salty Dog Talk: The Nautical Origins of Everyday Expressions" by Bill Beavis and Richard G. McCloskey (Sheridan House, Dobbs Ferry, N.Y., 1995. First published in Great Britain, 1983). http://www.phrases.org.uk/bulletin_board/28/messages/325.html UNDER THE WEATHER - "Ik Marvel, a pseudonym that resulted from a misprinting of J.K. Marvel, was the pen name of American author Donald Grant Mitchell. In his 'Reveries of a Bachelor' (1850) Ik Marvel is the first to record 'under the weather,' which has been a synonym for everything from 'ill and indisposed' to 'financially embarrassed' and 'drunk,' and has even been a synonym for 'the discomfort accompanying menstruation." From "Encyclopedia of Word and Phrase Origins" by Robert Hendrickson (Facts on File, New York, 1997). http://www.phrases.org.uk/bulletin_board/6/messages/274.html This phrase meaning ill or indisposed is an Americanism dating to 1827. From the Austin Papers of that year in a reference to the unsuccessful Fredonian Rebellion of 1826-27, when a small group of Texans attempted to oppose the Mexican government: "The fredonians is all here rather under the wether." The phrase probably derives from the idea that the weather can affect your mood and health. It is often thought to be nautical in origin, but there is no evidence of that. http://www.wordorigins.org/index.php/site/comments/under_the_weather/ Ailing, ill; also, suffering from a hangover. For example, She said she was under the weather and couldn't make it to the meeting. This expression presumably alludes to the influence of the weather on one's health. [Early 1800s] The same term is sometimes used as a euphemism for being drunk, as in After four drinks, Ellen was a bit under the weather. http://www.answers.com/under%20the%20weather

the phrase under the weather originally had nothing to do with weather. the correct phrase is under the wether. It refers to the fact that female sheep resist the efforts of the castrated male sheep to mount them. When the female is so ill that she cannot resist the wether's attentions, she is literaly under the wether.

It's a nautical term it comes from under the weather bow and it means the side of the ship that the bad weather is coming from