From the NCE manual:

"STD programming (option 1) will automatically determine whether to use the Direct or Paged programming methods. Paged programming is used by older decoders and can take up to fifteen seconds to read each CV. Direct mode is newer and generally reads CVs in one to two seconds. For various reasons you may wish to ‘force’ the programming method to one or the other types. You can press 4 for paged programming or press 5 for direct programming. Standard sets the most common decoder parameters." 

  • The timeout is largely dictated by the DCC standards governing both the acknowledgement mechanism from the decoder and the acknowledgement wait time for each query.
  • The DCC programming standards provide for acknowledgement by the decoder drawing a short current pulse.
  • This form of response cannot return multiple replies. So a response within the acknowledgement wait time is classified as a yes and no response by the decoder within the acknowledgement wait time is classified as a "no".
  • This acknowledgement wait time is specified in the DCC standards and cannot be changed in a command station.

The much slower wait timeout in Paged Mode is due to the way Paged Mode works. The only question that can be asked of the decoder is "Does CVn have a value of x?"

The only two responses the decoder can make is "yes" or silence. So before the command station can decide there is no decoder, it has to ask 256 questions, one for each possible value between 0-255 and wait for the acknowledgement wait time each after each question.

Direct Mode is much faster. This is because another question that can be asked of the decoder is "Is bit X of CVn ON?" The only two responses the decoder can make is still "yes" or silence. But it only takes around 9 questions to determine the value of CVn or there is no decoder.

From https://groups.yahoo.com/neo/groups/NCE-DCC/conversations/topics/102498