Pocketsphinx - Adding words and Improving accuracy
To improve accuracy you may want to try adapting the acoustic model to your voice. http://cmusphinx.sourceforge.net/wiki/tutorialadapt
To learn how to add new words: http://ghatage.com/tech/2012/12/13/Make-Pocketsphinx-recognize-new-words/
With something like this, you can't be certain, but I can offer the following suggestions:
Perhaps the language model somehow has low probabilities for "spaghetti" and "pencil". As you suggested, you could use a JSGF to test out how it does for recognition if it doesn't use the N-gram models, but instead does a simple grammar (give it like twenty words, including spaghetti and pencil). This way you can see if it is perhaps the language model which makes it difficult to recognize these words, and it can do okay if it considers all the words to have equal probability.
Perhaps you simply pronounce these words poorly, even with the alternative dictionary entries. Try either A. Testing other peoples' voices, or B. Adapting the acoustic model to your voice (see http://cmusphinx.sourceforge.net/wiki/tutorialam)
Also, what is it recognizing them as when it is failing? If possible, remove the words it misrecognizes as from the dictionary.
Again, for overall accuracy, only three things are going to really help you: restricting the grammar, adapting the accoustic model, and perhaps getting higher quality recording input.
Make sure you put a tab (not a space) after the word and before the start of the pronunciation.