Using MCP naming:

    ...
    this.field_72156_cr = true;
    ...
    }

That flag seems to tell the method setBlockBoundsBasedOnState() that it is being used by the above method, and thus should set the bounds differently than the full block size (which it should use at other times).

The ray trace method does not reset that flag once it is done. Thus, after the player first time aims at stairs block, the flag gets set, and the bounds will always return the setup for the last stage of ray tracing after that. (Except for the ray tracer itself, which will go through the stages at each call).

As a symptom, see comments in MC-1390 (water droplets generation calculates the start height too high).

Fix

        ...
        this.field_72156_cr = true;
        int var14;
        int var15;
        int var16;
        for (int var12 = 0; var12 < 8; ++var12) {
            ...
        }
        this.field_72156_cr = false; // FIX
        ...

Bug found and fix tested on version 1.4.7 while fixing MC-1390.