I've tried this, just out of curiosity, but it didn't work for me.
As I see, the command line suppose using of pipe encoding, but correct syntax of standard input (with ffmpeg) is 'pipe:0'.
For example, the following command line (in command prompt) works fine:
cat test.wav | ffmpeg -i pipe:0 -acodec alac output.m4a
The equivalent command line in MB however doesn't work, here is the log:
08.10.2010 01:36:16 - 5.1.2600.196608 - 1.2.3929.33619 - System.IO.FileNotFoundException: Could not find file 'C:\Documents and Settings\power\Local Settings\Temp\tmp6E.m4a'.
File name: 'C:\Documents and Settings\power\Local Settings\Temp\tmp6E.m4a'
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy)
at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share, Int32 bufferSize, FileOptions options)
at #=qKgrTK7xGiiM4vbusPi$3yMR7aaflot7crAEjt59qvOC341tihwMU_lfj3bMNxLov.#=qhm5pkZNpPfuSLyhX4VUAGg==(#=qmGKUPwli5HBdXh8eI9GfXYLUr$P0yozBKwZawwZM5iA= #=q5OvkMBvVTXL0Vw5OtTFgcA==, FileOptions #=q4$wvHzV0vM7p80uTBeqZug==)
at #=qn$dtZdXb3PUi5jUNwUSwy2c0NxEOagsVjP07cchTRqNoU101QTTKym5tROhwucHH.#=qKDYZxkNJpm9USAPfE_Ly_Q==.#=qbIaZVDt7KH9VZPbbOO4mGA==.#=qxMmApz21QxkbvhZu_Z130xKKKdIYOC5NI2lG3XIxstM=(#=qNbwa4gJtY7Rg8o8Ft7Rx4zaye14J9kf0naEj$M7vEcjNp4rVvFryxQ1QN6RfSXGq #=qT1YMmx$bOgmHJJZnpSIVqA==, List`1 #=qugjWC$GIWXZLg5m1JqCN5A==)
at #=qn$dtZdXb3PUi5jUNwUSwy2c0NxEOagsVjP07cchTRqNoU101QTTKym5tROhwucHH.#=qKDYZxkNJpm9USAPfE_Ly_Q==.#=qbIaZVDt7KH9VZPbbOO4mGA==.#=q4tz4byGu5W8AAk1sTkINeg==(#=qNbwa4gJtY7Rg8o8Ft7Rx4zaye14J9kf0naEj$M7vEcjNp4rVvFryxQ1QN6RfSXGq #=qb8BWKuUS2IPZ0TPINYwjkw==)
at #=qn$dtZdXb3PUi5jUNwUSwy2c0NxEOagsVjP07cchTRqNoU101QTTKym5tROhwucHH.#=q_lSHKdmUmHhErOEcuHRqEg==.#=qYP21w18KL0VFOf8ZvFEbfg==(#=qNbwa4gJtY7Rg8o8Ft7Rx4zaye14J9kf0naEj$M7vEcjNp4rVvFryxQ1QN6RfSXGq #=qg2EMmCfmJwhawMjG4MdDIg==)
at #=qn$dtZdXb3PUi5jUNwUSwy2c0NxEOagsVjP07cchTRqNoU101QTTKym5tROhwucHH.#=qpIgsTx2KCLEtAeNWXA_fgw==(#=qNbwa4gJtY7Rg8o8Ft7Rx4zaye14J9kf0naEj$M7vEcjNp4rVvFryxQ1QN6RfSXGq #=q54jl_LLiXSOaSSGZQNDm9w==)
at #=qKgrTK7xGiiM4vbusPi$3yMR7aaflot7crAEjt59qvOC341tihwMU_lfj3bMNxLov.#=qBniXPEZioo5XxV15kruNHg==(#=qNbwa4gJtY7Rg8o8Ft7Rx4zaye14J9kf0naEj$M7vEcjNp4rVvFryxQ1QN6RfSXGq #=qqOkV04xY5tlzKq2dgCc$yw==, Boolean #=qJspNdO8asy3XFuXNXW0RMZ1xBOVyvEfalgZ4TnDxzq4=)
at #=qNLJAyq_x8$6ipfK64TnRPjFTtZIHXJsAgath3FZHY36DVSyrxCIfQ4Kbkm45J5pK.#=q2$Ad$IL71oEaWtjIaknGYdrcRUJt_vajD0LU9fHA$14=(#=q108wQ_HGr3AX3vkfi2XSJg== #=qYN29chmN2je1R1xvygIUxA==, #=qNbwa4gJtY7Rg8o8Ft7Rx4zaye14J9kf0naEj$M7vEcjNp4rVvFryxQ1QN6RfSXGq #=qrkUN5Gvavs5fR65PRa7nvg==, Boolean #=qTp6XtMd2WEjDYqKDPAYpBKdsPSZVM7h9oz7wvcAs0hw=, List`1 #=q5IdMDO$IKez8B1lTNLDrjw==)
at #=qNLJAyq_x8$6ipfK64TnRPjFTtZIHXJsAgath3FZHY36DVSyrxCIfQ4Kbkm45J5pK.#=qRc199r5JTTWl2w0Sg5WrKg==(#=qNbwa4gJtY7Rg8o8Ft7Rx4zaye14J9kf0naEj$M7vEcjNp4rVvFryxQ1QN6RfSXGq #=q27PLOG_R_1wFkw8i$iHjaA==, Boolean #=qA6s9mMr1Bu15CJTXsxGHZ1RauwffC2yC19bo13VgazE=)
at #=qVbrkIxpXohgGdBuR3ulkwhONK1bfj5kwEV0kX9Z5WQQ=.#=q$xvi$SmChxFS1zJBpVK5vw==(#=qNbwa4gJtY7Rg8o8Ft7Rx4zaye14J9kf0naEj$M7vEcjNp4rVvFryxQ1QN6RfSXGq #=qqWE5lTvuo$c57hu_ietpqw==, Boolean #=qid6u0zP35W2XdvNNXHtkMj2X3XsLUGxJxmgdXfHKQWI=, Boolean #=qdW5yiJGeTAa3utEwCxTB$w==)
at #=q8kqtwm6MvhEyFa8ivQJqq6jNzfz03Ut7vPjRe3IroNY=.#=q5aUbGAPlGw_K3iWDR8EnJIJ89UELvlPQF66oqXvOtjI=(Object #=qaMrrcv46xIxKAO06ob9c5g==)
Additionally, it seems that ALAC doesn't benefit by lossyWav, so maybe this option should be removed from encoding profiles.
P.S. The same is true for APE, so if you, Steven decide to add support for Monkey's Audio, you should not add lossyWav as an option too.