As far as setting up those steps should be correct. It may be a problem with something external to UE4. I’m using Emscripten version 1.35.22 and my .emscripten file has all the paths set correctly:
import os
JAVA='F:/Emscripten/java/7.45_64bit/bin/java.exe'
SPIDERMONKEY_ENGINE='F:/Emscripten/spidermonkey/37.0.1_64bit/js.exe'
CRUNCH='F:/Emscripten/crunch/1.03/crunch.exe'
LLVM_ROOT='F:/Emscripten/clang/e1.35.0_64bit'
EMSCRIPTEN_NATIVE_OPTIMIZER='F:/Emscripten/clang/e1.35.0_64bit/optimizer.exe'
NODE_JS='F:/Emscripten/node/4.1.1_64bit/bin/node'
PYTHON='F:/Emscripten/python/2.7.5.3_64bit/python.exe'
EMSCRIPTEN_ROOT='F:/Emscripten/emscripten/1.35.0'
V8_ENGINE = ''
TEMP_DIR = 'c:/users//appdata/local/temp'
COMPILER_ENGINE = NODE_JS
JS_ENGINES = [NODE_JS]
I always delete temporary files when switching engine versions, so that’s not a problem. My browser versions are:
Firefox32: 43.0.4
Firefox64: 43.0.4
Chrome64: 48.0.2564.82 beta-m (64-bit)