I was never able to build FFMPEG for Android under Windows but successfully did so under Ubuntu (after having some hard time though).
I used Oracle VM Virtual Box freeware to emulate Ubuntu machine under Windows.
I then built FFMPEG using the scripts from bambuser http://bambuser.com/opensource.
I then moved the resulting directory into the windows under my project's jni folder and referred the libs from my Android.mk
FFMPEG_DIR := ffmpeg
ifeq ($(TARGET_ARCH_ABI), armeabi)
FFMPEG_DIR := $(FFMPEG_DIR)/armeabi
else
ifeq ($(TARGET_ARCH_ABI), armeabi-v7a)
FFMPEG_DIR := $(FFMPEG_DIR)/armeabi-v7a
endif
endif
include $(CLEAR_VARS)
LOCAL_MODULE := libavcodec
LOCAL_SRC_FILES := $(FFMPEG_DIR)/lib/$(LOCAL_MODULE).a
LOCAL_EXPORT_C_INCLUDES := $(LOCAL_PATH)/include
include $(PREBUILT_STATIC_LIBRARY)
include $(CLEAR_VARS)
LOCAL_MODULE := libavcore
LOCAL_SRC_FILES := $(FFMPEG_DIR)/lib/$(LOCAL_MODULE).a
LOCAL_EXPORT_C_INCLUDES := $(LOCAL_PATH)/include
include $(PREBUILT_STATIC_LIBRARY)
include $(CLEAR_VARS)
LOCAL_MODULE := libavdevice
LOCAL_SRC_FILES := $(FFMPEG_DIR)/lib/$(LOCAL_MODULE).a
LOCAL_EXPORT_C_INCLUDES := $(LOCAL_PATH)/include
include $(PREBUILT_STATIC_LIBRARY)
include $(CLEAR_VARS)
LOCAL_MODULE := libavfilter
LOCAL_SRC_FILES := $(FFMPEG_DIR)/lib/$(LOCAL_MODULE).a
LOCAL_EXPORT_C_INCLUDES := $(LOCAL_PATH)/include
include $(PREBUILT_STATIC_LIBRARY)
include $(CLEAR_VARS)
LOCAL_MODULE := libavformat
LOCAL_SRC_FILES := $(FFMPEG_DIR)/lib/$(LOCAL_MODULE).a
LOCAL_EXPORT_C_INCLUDES := $(LOCAL_PATH)/include
include $(PREBUILT_STATIC_LIBRARY)
include $(CLEAR_VARS)
LOCAL_MODULE := libavutil
LOCAL_SRC_FILES := $(FFMPEG_DIR)/lib/$(LOCAL_MODULE).a
LOCAL_EXPORT_C_INCLUDES := $(LOCAL_PATH)/include
include $(PREBUILT_STATIC_LIBRARY)
include $(CLEAR_VARS)
LOCAL_MODULE := libswscale
LOCAL_SRC_FILES := $(FFMPEG_DIR)/lib/$(LOCAL_MODULE).a
LOCAL_EXPORT_C_INCLUDES := $(LOCAL_PATH)/include
include $(PREBUILT_STATIC_LIBRARY)