1999 Mazda B4000 4x4 4.0L 75000 km's
Trans will shift thru all 5 gears when cold. Let engine/trans get up to operating temp plus another 10 km, leave from a stop and you will get 1-3 shift skipping 2nd gear. No DTC's stored but I do get a flashing O/D light sometimes when I use moderate or WOT position. With o/d off and a WOT test run I do get a flare coming out of second shift. The oil has been changed at 25000 km intervals. Oil pan always clean. I have read thru the VB diary (which is excellent). Do you think I might have a damaged seperator plate gasket that might cause this problem? When the O/D light is flashing, what is that telling me other than it has gone into limp mode?

If you get a flashing O/D light, you should have codes stored in the PCM. You can scan for codes to see what problem(s) are reported by the PCM.

I have an Equus Innova 1300 OBD ll code reader but it is not picking up any codes. The instruction manual says I should get (PCM) PO & Pl codes but I guess cause the check engine light is not on that my reader cannot access the trans codes which the flashing O/D light is indicating.

Do you get 5th gear when 2nd is missing? 2nd gear in the 5R55E is an overdriven gearing arrangement so it uses the Overdrive band. That same band is applied in 5th gear. Often a lack of one will show up as a lack of the other as well. Sometimes that can be a SSC solenoid failure... could also be a servo leak, and yes could be other valve body issue as you have mentioned.

Maybe your scanner can only read the "standard" OBD II codes, but the transmission codes are the "extended" Ford codes. e.g. a standard OBD code would be something like P0702, but the trans code would be P1172 or similar. Bummer.

Yes I get 5th when 2nd missing. I can get 2nd manually anytime hot or cold. Using deductive reasoning, can I assume that the overdrive band and the servo are ok if I get 5th?
Sorry gent's, I figured that this thread was closed due to site upgrade. I started a new post in the trans forum.

It does seem to me that if 5th is ok, but 2nd is not, then it would point to an issue with the valve body (gasket, separator plate) rather than the band or servo.

Also, the hot/cold nature of the problem would indicate that it may be related to

a) expansion of components and/or b) viscosity of the ATF