I found a simple way to fix the bug, which apparently occurs only on windows98 (95,ME) in the Fasm IDE if one tries to replace sequences of strings with the replace dialog. Since somewhere between version 1.46 and version 1.55, the IDE quits prematurely after the FIRST replace is done even if one clicked "yes" to continue.
This behaviour is caused due to a bug (destroyed registers) in the message handling from Windows 98.
A simple workaround would be to change just 3-4 lines in the FasmW.asm file:
(old code starting at line 1368)
.replace:
invoke SendMessage,ebx,EM_REPLACESEL,TRUE,replace_string
.replace_next:
should be changed into:
.replace:
push ebx edi
invoke SendMessage,ebx,EM_REPLACESEL,TRUE,replace_string
pop edi ebx
.replace_next: