Your interesting/significant question a little seem to be a little complicate (at least based on my perception), but I strive to answer it by giving some related points. (Note that my answer is according to Shia Islam)
Firstly, note that there are 2 sorts of Istikharah,
1: Asking Khair (blessing) from Allah which is related to everything,
and is not exclusively regarding doubt.
2: Istikharah in doubt situation
Secondly, concerning Istikharah (No.2) which is in doubt status, it is done as the final step, namely: you ought not to do it if you have not done 2 previous steps of that. And actually before Istikharah, you should use thinking about the issue, then –if you didn’t conclude-, consulting to aware (related) individuals, then it is better if you prayer+Zikr-Istikharah, afterwards (in such positive-holy situation of praying, look at your inside and feel which way/item your inside is more inclined to, then do that. If you were still confused/doubted about which way you should choose, afterwards use Istikharah by Quran.
Of course, Kilise mentioned some assumptions which seem to be profit. Anyhow, the significant point which ought to be paid attention is that Istikharah (as much as I’ve perceived) is not like sortes/augur or prediction, but it just help us in the situations which we are doubted (e.g.) doing/choosing 2 issues or practices, then Istikharah help us to choose the more appropriate way (and actually helps us to exit from such confusing position.
Meanwhile, to the best of my knowledge, there is no guarantee in the accuracy of the Istikhara if we directly refer to it (without passing its previous steps such as thinking/consulting to aware related individuals and …). Besides, AFAIK, Allah asks us not to use Istikharah as much as possible and factually use/apply our mind/intellect/decision (+consulting) instead of that, and in truth it ought to use just in really doubt situation, otherwise its response might be …
Eventually, by doing Istikharah (in its accurate way), it will indicates/helps you to choose the best way for you (that you really have very doubt about the best way). But the significant point is that:
Perhaps, occasionally, you follow the result of Istikhara, but you apparently assume that the helping/result of Istikhara wasn’t be profitable for you, but the fact is that:
Your profits (that Allah knows everything) was not in that, and actually if you would choose the other way (against Istikharah), its consequence would be harmful for you (in long-term period) …
God willing it can help you to some extent.
Source: www.islamquest.net (in Arabic/Farsi)