I agree with Jan's comments.
To amplify and clarify the point about setting varialbes in HL7.php...
* make an HL7 class.
* make these variables properties of that class, eg:
var $_Net_HL7_REPETITION_SEPARATOR"] = '~';
* then, to change these settings use an options array to the constructor or a setOption() method. See how PEAR::DB handles this.
In addition, use ' instead of " when you're not evaluating variables in the string.
Note, the directory in the PEAR CVS repository will be Net_HL7, not Net/HL7.
You have "Copyright (c) 1997-2004 The PHP Group" in the header. Is that really what you intend?
Some of your docblocks don't have short description -- for example Net_HL7_Message(). The first line should be a quick sentence. The full description should follow in a separate paragraph. See the "Sample File" in the coding standards on how to make them
Add docblocks for all the var declarations.
Lowercase your boolean constants: "True" should be "true" and "False" should be "false."