@dionysia, ratvn, RosinedUp: You've got it. 

The Equal Tempered scale system is a compromise, that is easier to manufacture pianos, electronic keyboards, tuners and etc for.  It has some advantages of no notes sounding bad enough to need to be avoided as "wolf notes" (not to be confused with wolf tones, which are a different sort of problem), but it achieves this at a cost.. Music played equal tempered may sound and feel a bit different than when it was written.  For example, you may be familiar with a piece by Bach, "The Well Tempered Clavier"?  The whole point of that piece is it was composed to show yet another type of temperament, the wohltemperiert or "Well Tempered" system.  It doesn't just mean that the clavier (a type of keyboard instrument from that time) doesn't get annoyed easily.  LOL  But if it is played with equal temperament, like on a typical modern electronic keyboard or something?  It is just not going to have the sound that he intentionally wrote the piece to showcase.

One of the advantages of the violin (and violas, cellos, etc) is that they can play using any of the temperament systems.  That is one of the things about the violin that kept making me want to learn to play it, as I learned more about music theory.  Like the human voice, any violin can play using any of the systems and all of the "colors" that different key signatures may have in systems other than the modern Equal Temperament. 

That is a phenomenal advantage in such a small and portable instrument.  "Expressive Intonation".  The ability to alter pitch of notes to make them feel more sad or joyous (for example), as easily as the violin can play at different volume levels for purposes of musical dynamics.  Add that to the violin's rather wide timbral range that can be controlled by whether one bows closer to the bridge or the fingerboard, and you have an instrument with amazing capabilities.  And in such a small package, weighing around one pound, and (at least for acoustic violins), no batteries required!  LOL

That is one of the major reasons I finally decided a little less than a year ago to try and learn violin.  But probably not the reason that most people do, I am guessing from what I see discussed in most violin forums on the net. 

It isn't a huge difference, KindaScratchy.  In many cases it is more like "leaning" slightly than actually trying to play a different intonation.

If the notes you are feeling a need to adjust a little bit from your muscle memory are in pieces you might be familiar with as vocal melodies or something like that, then your ear is probably telling you right.  Unless they have been "auto-tuned" or trained extensively against piano notes, most singers don't actually sing perfectly in Equal Temperament.  Equal Temperament is easy for things like computers or inexpensive electronic tuning machines, but it doesn't sound "natural" to most people's ears.  Singers usually will instinctively flex the pitch as part of expression. 

When in doubt, I feel it is always better to trust your ears than a tuning machine.  Machines are not known for their musical taste.