Orthotics are designed to provide exacting control on one's foot structure.  This is accomplished by creating the orthotic from a mold of one's foot while it is held in a corrected position.  Since the orthotic is shaped exactly to one's foot, it should be completely comfortable to wear.  Some people do require a break-in period initially in order to get used to the presence of their orthotics, but this generally lasts only 2-3 weeks, and most people can wear orthotics from the beginning without discomfort.  However, there are times in which discomfort can develop that a break-in period cannot change.  The reasons for this discomfort vary, but nearly always have to do with how the orthotic interfaces with a specific shoe.  The following discussion details some of these more common reasons for orthotic discomfort, and how they can be solved.

The arch feels like it is too far forward on the orthotic.
This situation commonly occurs when the shoe that is being worn is sized too large.  Many people make the common mistake of either not knowing their current actual shoe size, or purchasing larger shoes to obtain greater width instead of simply purchasing a shoe in their size that is wider.  Even a half size too large can allow the foot to slide forward in the shoe like a piston.  When the foot slides forward, the orthotic slides forward as well.  As the foot then slides back, the orthotic may stay in that forward position, leading to the feeling that the arch is too far forward.  The movement will create discomfort in the arch, and limit the effectiveness of the orthotic.  This is solved by ensuring the proper sized shoe is worn, so the foot and orthotic stay in place like they should.

The heel feels like it pops out of the shoe when the orthotic is in it.
Some shoes, especially slip-on styles, have a limited capability to stabilize the foot in the shoe.  The foot is not locked down in back, only being secured over the middle and front by the top of the shoe.  When adding an insert to those types of shoes, a form of instability can develop at the back end of the shoe and the heel can 'pop' out of the shoe easier than when the shoe does not have an insert filling out the inner surface.  The simple solution is to convert to a lace up shoe where the tightness and stability of the upper part of the shoe is controlled by tightening the lacing.  Another alternate is to choose a slip on shoe with an extra deep foot well.  Unfortunately, some styles of slip on shoes simply will not work with orthotics, and should be avoided.
When this popping occurs in a lace up shoe, a number of factors could be at fault, including shoe width issues, heel width issues, and shoe size issues.  Sometimes, shoes simply fit the foot in a manner that is incompatible with an orthotic, and a different shoe should be selected that fits the foot, orthotic, and shoe together in a more cohesive manner.  An alternate option is to try a self-adhesive felt pad under the tongue of the shoe.  This will push the front of the ankle down, and help settle the heel back into the shoe.

The front edge of the orthotic pinches the skin at the ball of the foot.
This does not frequently occur, but can be annoying nonetheless.  The end edge of the orthotic can be felt in this scenario, and can physically pinch the skin just behind the bases of the toes.  This may be due to a number of factors, including orthotics that are slightly too long, but more commonly it is related to small amounts of excessive foot motion in the shoe.  To remove this irritation, the use of a soft top cover over the orthotic plate may help.  If there is an actual problem with the orthotic length, the end can be ground down to a shorter length.

The orthotic feels too prominent on either side of the foot.
Orthotics are prescription devices, and the angle of the arch control they exert from one side to another is built into the prescription.  There can be times in which only a degree or two of error can result in discomfort, with a feeling that the orthotic pushes too far on one side or the other.  A simple solution is to use a cork bar or other such modification under one side of the orthotic to reduce pressure to the other side that feels too prominent.  This often works well, and is easy to adjust.  If the degree is too severe, than the casting needs to be repeated and the orthotic needs to be remade.  Sometimes the foot conditions the orthotic is being used to treat can be the source of discomfort if they have not been resolved yet.  For example, orthotics are commonly used to control plantar fasciitis.  If the inflammation of the plantar fascia has not fully been resolved by the other treatment measures used in this condition, then the presence of the orthotic plate can irritate the still inflamed fascia and cause discomfort on the inner side of the foot.  By fully treating these conditions and resolving the inflammation, the orthotic will become comfortable to wear.

The orthotic makes a burping or squeaking sound with every step.
The reason for abnormal sounds during orthotic wear usually has to do with the transfer of air under the orthotic plate.  It is difficult to control, but the use of baby powder in the shoe may help reduce this air motion.  Also, having a soft cover put on the top and bottom of the orthotic may reduce the sounds as well.