Answer
ArcPad is configured to give you elevations in Height Above Ellipsoid (HAE). You may be able to change this to Mean Sea Level (MSL) if you have the appropriate version of software.
Solution
ArcPad 6.0 or earlier
You can’t do anything in ArcPad or the GPS to get MSL elevations. In ArcMap you could create an attribute for MSL and calculate values using procedures and the equation stated below.
ArcPad 7.0 or higher
- Â Locate a few points around your study area and write down the Lat/Lon values.
- Follow this link and input your values  http://www.ngs.noaa.gov/cgi-bin/GEOID_STUFF/geoid03_prompt1.prl
- You may want to take an average of these points
- Open ArcPad
- Click the dropdown arrow next to the satellite button
- Select GPS Preferences
- Click on the GPS Height tab.
- Enter the Geoid Separation Value given to you from the website.
ArcPad determines the Z value by this equation
 Z value (MSL) = HAE –  Geoid Separation – Antenna Height
Navigate to this link and download the pdf.  Page # 46(52)  talks about this in more detail.
http://downloads.esri.com/support/documentation/pad_/ArcPad_RefGuide_1105.pdf