I don't think it is that unusual, ladyeclectic.  Even after over 30 yrs of playing guitar and other instruments, when I started playing violin/fiddle I ran into achey shoulder, kinks in my neck, weird aches in wrist and elbow and especially... The thumb muscles, because of the infamous "death grip".  LOL  There was this one section of muscle at the base of the thumb that would just burn after I'd played for only 10 or 15 minutes.

I found it very annoying, since I have strong hands, and I'm used to being able to play for quite a while without fatigue.  But the violin, it was kinda like starting music over.  I had to figure out how long I could actually practice/play before needing to take a break, and to avoid needing long breaks, I broke my practice and exercises down into 5 minute mini-sections and over the first year I worked my violin practice time up from 15 min to 45 min a day.  It took patience and I found it very aggravating. 

Basically, you have to be gentle with yourself, while persistent about practising.  Try and find how much you can do at one time right now *before* you run into discomfort or pain (including pain later).  Get a timer if necessary, and stop yourself before that point.  Let the muscles and joints have time to heal, grow and adapt to the new strains and odd positions.  You may be able to do a few short sessions spread out through the day with less trouble.

If you end up overdoing anyway, then take it real easy for a day or few.  In the long run, it adds up to getting more practice/playing time, since you will definitely end up getting less if you give yourself an injury that has to be rested for weeks or even months.

Pain is a warning sign, though.  No extra points are awarded for ignoring it, and any good teacher won't advise you to ignore it (unless they like lawsuits).  Check your method/technique/form, and back off and rest when something starts to hurt, or better *before* it starts to hurt.

That isn't just for beginners, though.  Denny already told of some wrist troubles, and I recently ran into some myself.

I've been playing violin for 3 yrs, and guitar since 1976, so def not really a noob.  A few months ago I ramped up my practice routines with a lot more time spent on scales and exercises.  Like some hours on just scales and exercises every day and pushing up metronome speeds, as well as regular playing.  I was getting into feeling "serious", you understand.

Started getting some tingles and aches and numbness in my left hand.  Nothing major, and I figured it was just fatigue.  So I gave it the popular thought "What doesn't kill me just makes me stronger" and tried to blast through that "barrier".  The next day my wrist was swollen and inflamed and even doing just everyday non-musician stuff was disturbingly painful.  Like cutting an onion with a kitchen knife or buttoning a shirt being difficult and painful for that hand.

Now, I may do some silly/stupid stuff trying to "feel" serious, or to think of myself as serious in ego-gratifying ways.. But when it comes right down to it, I am very serious about my music and my playing.  So I called my doctor and got it looked at and got referral to a specialist for x-ray and ultrasound pics and then regular appointments with a physical therapist.

On the good side, it wasn't carpal tunnel, as I had been worrying.  On the not so good side, it was seriously overstrained and inflamed and probably due to the "repetitive stress".  At first my PT said to cut down to an hour a day of playing (that's combined, all instruments, not an hour of each, I asked).  That and the stretching exercises showed some improvement by the next appointment, but not enough for her to be happy (and I still couldn't play much or for long without pain, even with ibuprofen).  So she asked me to take a week completely off from playing and to use that hand as little as possible other than stretching exercises several times a day.  Which became two weeks.  Then almost a month before the wrist has recovered enough that finally I could start playing again, carefully, and I'm working my time up gradually now.  Carefully.

In all honesty, it might not have taken that long if I hadn't "cheated" a few times and played anyway.  But hey, family and Thanksgiving and a couple visits from musician friends.. I knew I was risking additional setbacks, even keeping it to short sessions of just a couple songs at a time.  And I got them.  No big surprise there.

I'm doing ok now.  Using a timer to remind myself to take breaks and not get so lost in playing that I lose track of time, wearing a brace on that wrist when I sleep or practice or do anything else that is repetitive.  I'm back up to being able to play a few songs at a time and then rest and play some more, and being able to spend at least a few minutes a day on "repetitive stuff" like scales and exercises.  Which feels great after being shut down for over a month.

You don't want to deal with that.  Nobody does.  So don't push yourself too hard, and if something starts to hurt, back off, make sure you're doing everything right and take it easy.  If it keeps happening, see a doctor and make sure nothing is going badly wrong.

No extra gold stars are getting handed out in music for risking doing yourself some damage so you can't play.