You need to ask questions whenever you hear an unknown acronym, and you need to do so ASAP. The first weeks on this job will set much of the tone and tenor of your employment with the company, and things will fare far worse if you are making mistakes as opposed to asking questions.
Importantly, when you ask questions about an acronym, try to avoid asking it again by jotting down definitions for future reference. Companies are little societies, complete with their own culture, values, and lingo. Acronyms are part of what separates this company from others, and the sooner you pick up the language, the sooner you will feel a part of the company rather than apart from it
At the same time, companies should make a real commitment to easing the transition and assimilation of new employees. After all, an excellent orientation program can play a key role in controlling turnover. When companies use acronyms as you describe, it is either an unintended oversight or a willful exclusion to separate insiders from outsiders.
Either way, you should suggest to your manager or Human Resources representative that it would be helpful to have a glossary of company-specific terms for new hires. Hopefully they will not gloss over your idea for a glossary.
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