It is tricky to figure out the cause for this, but I suspect there is something going on with the conversion of coordinate systems (Y up vs. Z up).
Assuming that the BIN file contains Y up positions, you would expect the world Z axis to end up as the negative Y axis in Max, and the world Y axis from the original scene to translate to the positive Z axis in Max. There are two ways to shift the coordinates in the PRT Loader - either by transforming the scene object by the correct matrix, or by using a KCM to swap the Y axis for negative Z and the Z axis for positive Y.
The transformation matrix to convert from Y up to Z up would be, in MAXScript,
(matrix3 [1,0,0] [0,0,1] [0,-1,0] [0,0,0])
For example, if you have a point with coordinates [1,2,3], then
[1,2,3] * (matrix3 [1,0,0] [0,0,1] [0,-1,0] [0,0,0])
[1,-3,2] --> the X axis remains the same, the Y axis in Max is the -Z axis from the source, the Z is the Y.
The KCM just took the Position channel, used ToScalar to split the X, Y and Z components and combined the X, the -Z and the Y using ToVector which was output back as Position. The resulting particle placement matched the result from the the above transformations (transformations were of course disabled while running the KCM).
In both cases the resulting particle positions were rotated at 90 degrees relative to the fluid mesh/PRT Loader you posted, so there must be something wrong in the way the BIN file was exported, or the way we are converting the coordinate systems.
I am not an expert when it comes to RealFlow, so I wonder if there is anything special about the way that BIN file was created that would explain the 90 degrees rotation about the vertical axis I am seeing… This does not explain why the particles are off compared to the source (as no scale factor can bring them where they belong visually), but if the rotation doesn’t make sense, I cannot even start figuring out the other problem. Also, are we absolutely sure the BIN file contains the exact same particles (same frame) as the screenshot you posted from Houdini? They appear similar, but not 100% the same. For example, in the center back there is a small “hill” covered with particles in Houdini, but with absolutely no particles in your Max Krakatoa rendering. So I wonder if the frame 0001 you sent really contains the particles we see in Houdini…