At first pass, this may seem like an odd combination of issues, but company culture has to be accounted for when changing accounting systems.
Change Is Scary
Your accounting staff is probably very comfortable with the status quo. Even though trying to extract data from your start-up bookkeeping tool and wrangling it into spreadsheets creates a lot of work and tedium for everyone involved, it is a familiar task. Logically, the entire staff may understand that the upgrade to SYMPAQ will enhance DCAA compliance, improve reporting, and reduce work for everybody. But it is still change, and change can be scary. Also, your staff may be comfortable with how you do business today, but are not excited about the effort and work involved to adapt to how you'll do business tomorrow. We'd like to believe that most will embrace the opportunity to improve internal operations, however, the real world doesn't work that way. Many people are quite content with the status quo and some are willing to walk away and seek employment elsewhere.
Ignorance Is Bliss
What you don't know can't hurt you right? If your company has been growing quickly, your staff is probably operating at maximum capacity just to keep up. If you are busy and growing, then all of your projects must be well run, right? Well, what if they aren't? Accounting software without rigorous internal controls make it easy to cover up mistakes or malfeasance by "cooking the books" after the fact. A compliant cost accounting system doesn't allow for that. Everything will be captured in an audit trail; making it much harder to hide the truth.
If it's hard to get visibility into project performance, then it is hard to see problems looming on the horizon. Likewise, it is hard to hold anybody accountable for the failure (or success) of any individual project.
Upgrading accounting software, or any major internal system, involves many procedural and operational challenges. Your company must adequately plan for the conversion to realize the benefits. Don't forget about your people though. If they aren't on board, the upgrade will go poorly - or fail.