If you are using Windows XP then you should try the Command Prompt first.

We tried running at the command prompt, but this suite of DOS programs doesn't work in the command line world of Windows XP

Lisequinn wrote:

We tried running at the command prompt, but this suite of DOS programs doesn't work in the command line world of Windows XP

"It doesn't work" isn't terribly specific. Does it give you some kind of error message?

Anyway, parallel port passthrough requires the "Megabuild" of DOSBox. As per Parallel port passthrough (Windows only) , you will also need Porttalk. In fact, Porttalk alone might be enough to get your program working from the XP command prompt, depending on how it "doesn't work".

Depending on the nature of the "hasp" (did you mean "dongle" ?) there may be other ways around it, but since you do have a controller card, there may be hope for this method.

The screen that comes up with the control panel of the program so that you can manipulate the data files from the flow cytometer, comes up mangled, without it's buttons and test and it's all garbled. it's frozen and you cannot interact with this. This problem is known and the programmers, they are not interested in fixing this, that is why I was hoping that we can use DOSbox. When we run it in DOSbox, the program comes up fine, but then complains that the hasp is not found. HASP - Hardware Against Software Piracy - also generically called a dongle.
I will try the Megabuild instructions.

Here is the config file portion that I am not sure how to edit correctly. I want LPT 1 to be active so that I can print via this parallel port. Currently, with this config I can't - Dosbox cannot find LPT1 (or any other LPT)

Timer and interrupt latency patch, fixes certain games
Add the 'IMGMAKE' command (creates disk images)
Make vgaonly features availible to other graphics cards - see [render]
Free choice wether 9-pixel wide characters should be used
Add DATE and TIME commands, midnight overflow, and host time synchronization
NE2000 Ethernet passthrough
OPL chip passthrough
Parallel Port passthrough and Virtual Printer patch, logging enabled
Parallel Port data redircetion to file/device
Add restart capability, Win95 can shutdown DOSBox through APM
Serial logging capability enabled
Increase maximum resolution to 1600x1200, add lot's of highres VESA modes
Add back selection of video memory size - up to 8MB = 1600x1200@32bpp
EGA / SVGA_S3 compatibility, enable LDGFXROM
CGA video memory slowdown
DOSBox can load while the splash screen displays
FILES= adjustable by Kippesoep
Restart capability - ctrl+alt+POS1 or config -r [params] or FJMP F000:FFF0
---
CONFIG:Loading primary settings from config file C:\Documents and Settings\admqu
inn\Local Settings\Application Data\DOSBox\dosbox-SVN_MB6.conf
MIDI:Opened device:win32
Invalid type for LPT1.
WinPcap has to be installed for the NE2000 to work

What am I doing wrong??!

That doesn't look like a config file; that looks like part of the documentation. Your config file is C:\Documents and Settings\admquinn\Local Settings\Application Data\DOSBox\dosbox-SVN_MB6.conf , like it says.

The config file will have a section preceded by "[parallel]". There are many threads about it, such as Printer question about h-a-l-9000's Mega Build and OLD CAD APP - Need to print to LPT1 (printer port) .

Don't forget, you need PortTalk.