I rrecently finished putting together a bike with parts from my 99 Cannondale, and other pieces salvaged from upgrades to my son's bike, onto a Sette aluminum frame. The bike is a back up bike for myself or my sons, who might need it as a spare. The 9 speed shifters and derailleurs are 105's. The chain is new and the 9 speed 12 x 25 cassette is fairly new. The bike shifts very well except it skips the next to last cog and goes right to the 25 cog. It while shifting up or down. If I adjust it so that it will grab the next to last cog it will not jump into the 25 cog unless I hold the shifter in. Is the front brifter shot? I can't think of any other adjustment to make that would effect the one cog and not the others.

Did you use new cables and housing? Did you set up your rear derailler per the Park Tool instructions (set limit screws first without cable attached, then attach cable and add tension)?

I did put new cables and Jagwire housing on the bike. However, I did not set the limit screws prior to attaching the cable. Would the limit screws make a difference shifting into gears within the limit range?

The bike shifts into the tallest gear and smallest gear. While riding I can put my finger on the shifter cable and pull it slightly and the derailer will shift the chain to the next to last cog, but I have to hold it to keep it from shifting back down.

I guess the first thing to do is the verify that all of the detents in your shifter are working. Detach the cable and push the small paddle until it stops clicking while pulling on the cable. Keep pulling on the cable and shift using the brake lever. You should be able to feel 8 clicks. If you only get 7, try flushing the shifter with WD-40 and see if you get that missing click back.

Once you have 8 clicks, use the Park Tool instructions to set the rear derailler. The high limit screw setting is critical to getting the indexed shifting set up properly. Every other shift will be affected to some extent if this screw is not properly set. The low limit screw only affects shifting into the largest cog. Proper cable tension is necessary because if there is any slack, your first and possibly second shift won't move the derailler the proper amount and your indexing will be off for all of the later gears.

My guess is that you have your high limit screw set out too far and are relying on cable tension to position the rear derailler. Because you are relying on cable tension, you have the tension set slightly too high and the problem compounds itself as you shift through the gears. By the time you get to the end of the cassette, you end up skipping a gear because the indexing is so far off.